============================================================ | | | Crystallography & NMR System (CNS) | | CNSsolve | | | ============================================================ Version: 1.3 Status: General release ============================================================ Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve,J.-S.Jiang,J.M.Krahn, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, G.F.Schroeder, T.Simonson, G.L.Warren. Copyright (c) 1997-2010 Yale University ============================================================ Running on machine: master3.bw03.cabm.rutgers.edu (x86_64/Linux,64-bit) with 8 threads Program started by: gliu Program started at: 16:49:21 on 28-Feb-2011 ============================================================ FFT3C: Using FFTPACK4.1 CNSsolve>{+ file: generate.inp +} CNSsolve>{+ directory: general +} CNSsolve>{+ description: Generate molecular topology file and/or generate coordinates for unknown atoms +} CNSsolve>{+ comment: CNSsolve> For most cases the generate_easy.inp input file should be used. +} CNSsolve>{+ authors: Paul Adams and Axel Brunger +} CNSsolve>{+ copyright: Yale University +} CNSsolve> CNSsolve>{- Guidelines for using this file: CNSsolve> - all strings must be quoted by double-quotes CNSsolve> - logical variables (true/false) are not quoted CNSsolve> - do not remove any evaluate statements from the file -} CNSsolve> CNSsolve>{- Special patches will have to be entered manually at the relevant points CNSsolve> in the file - see comments throughout the file -} CNSsolve> CNSsolve>evaluate ($par_nonbonded = "PARAM19") EVALUATE: symbol $PAR_NONBONDED set to "PARAM19" (string) CNSsolve> CNSsolve>{- begin block parameter definition -} define( DEFINE> DEFINE>{============================== important =================================} DEFINE> DEFINE>{* Coordinates for molecules of the same type (eg. all protein, all DEFINE> nucleic acid etc) can be input in the same coordinate file if the DEFINE> different chains are separated by a TER card or each chain has DEFINE> a different segid or chainid. *} DEFINE> DEFINE>{* A break in a chain can be detected automatically or should be delimited DEFINE> by a BREAK card. In this case no patch (head, tail or link) will be DEFINE> applied between the residues that bound the chain break. *} DEFINE> DEFINE>{* If a segid is present in the coordinate file it will be read unless DEFINE> segid renaming is used below. If renaming is used then all chains in a DEFINE> coordinate file will be given the same segid. *} DEFINE> DEFINE>{* If a PDB chain identifier is present in the coordinate file then this DEFINE> can be used for the segid *} DEFINE> DEFINE>{* NB. All input PDB files must finish with an END statement *} DEFINE> DEFINE>{============ protein topology, linkage, and parameter files =============} DEFINE> DEFINE>{* topology files *} DEFINE>{===>} topology_infile_1="CNS_TOPPAR:protein-allhdg5-4.top"; DEFINE>{===>} topology_infile_2="CNS_TOPPAR:water-allhdg5-4.top"; DEFINE>{===>} topology_infile_3="CNS_TOPPAR:ion.top"; DEFINE> DEFINE>{* linkage files for linear, continuous polymers (protein, DNA, RNA) *} DEFINE>{===>} link_infile_1="CNS_TOPPAR:protein-allhdg5-4.link"; DEFINE>{===>} link_infile_2=""; DEFINE>{===>} link_infile_3=""; DEFINE> DEFINE>{* parameter files *} DEFINE>{===>} parameter_infile_1="CNS_TOPPAR:protein-allhdg5-4.param"; DEFINE>{===>} parameter_infile_2="CNS_TOPPAR:water-allhdg5-4.param"; DEFINE>{===>} parameter_infile_3="CNS_TOPPAR:ion.param"; DEFINE> DEFINE>{====================== other linkages and modifications ==================} DEFINE> DEFINE>{* extra linkages and modifications by custom patches *} DEFINE>{===>} patch_infile=""; DEFINE> DEFINE>{============================ protein files ================================} DEFINE> DEFINE>{* Multiple coordinate files of the same type can be defined by duplicating DEFINE> all of the entries below and incrementing the file number *} DEFINE> DEFINE>{* protein coordinate file *} DEFINE>{===>} prot_coordinate_infile_1="template_hr64.pdb"; DEFINE> DEFINE>{* rename segid *} DEFINE>{+ choice: true false +} DEFINE>{===>} prot_rename_1=false; DEFINE> DEFINE>{* new segid *} DEFINE>{===>} prot_segid_1=""; DEFINE> DEFINE>{* convert chainid to segid if chainid is non-blank *} DEFINE>{+ choice: true false +} DEFINE>{===>} prot_convert_1=true; DEFINE> DEFINE>{* separate chains by segid - a new segid starts a new chain *} DEFINE>{+ choice: true false +} DEFINE>{===>} prot_separate_1=true; DEFINE> DEFINE>{========================= nucleic acid files ==============================} DEFINE> DEFINE>{* Multiple coordinate files of the same type can be defined by duplicating DEFINE> all of the entries below and incrementing the file number *} DEFINE> DEFINE>{* nucleic acid coordinate file *} DEFINE>{===>} nucl_coordinate_infile_1=""; DEFINE> DEFINE>{* rename segid *} DEFINE>{+ choice: true false +} DEFINE>{===>} nucl_rename_1=false; DEFINE> DEFINE>{* new segid *} DEFINE>{===>} nucl_segid_1=""; DEFINE> DEFINE>{* convert chainid to segid if chainid is non-blank *} DEFINE>{+ choice: true false +} DEFINE>{===>} nucl_convert_1=true; DEFINE> DEFINE>{* separate chains by segid - a new segid starts a new chain *} DEFINE>{+ choice: true false +} DEFINE>{===>} nucl_separate_1=true; DEFINE> DEFINE>{============================= water files =================================} DEFINE> DEFINE>{* Multiple coordinate files of the same type can be defined by duplicating DEFINE> all of the entries below and incrementing the file number *} DEFINE> DEFINE>{* water coordinate file *} DEFINE>{===>} water_coordinate_infile_1=""; DEFINE> DEFINE>{* rename segid *} DEFINE>{+ choice: true false +} DEFINE>{===>} water_rename_1=false; DEFINE> DEFINE>{* new segid *} DEFINE>{===>} water_segid_1=""; DEFINE> DEFINE>{* convert chainid to segid if chainid is non-blank *} DEFINE>{+ choice: true false +} DEFINE>{===>} water_convert_1=true; DEFINE> DEFINE>{========================= carbohydrate files ==============================} DEFINE> DEFINE>{* Multiple coordinate files of the same type can be defined by duplicating DEFINE> all of the entries below and incrementing the file number *} DEFINE> DEFINE>{* carbohydrate coordinate file *} DEFINE>{===>} carbo_coordinate_infile_1=""; DEFINE> DEFINE>{* rename segid *} DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_rename_1=false; DEFINE> DEFINE>{* new segid *} DEFINE>{===>} carbo_segid_1=""; DEFINE> DEFINE>{* convert chainid to segid if chainid is non-blank *} DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_convert_1=true; DEFINE> DEFINE>{======================== prosthetic group files ===========================} DEFINE> DEFINE>{* Multiple coordinate files of the same type can be defined by duplicating DEFINE> all of the entries below and incrementing the file number *} DEFINE> DEFINE>{* prosthetic group coordinate file *} DEFINE>{===>} prost_coordinate_infile_1=""; DEFINE> DEFINE>{* rename segid *} DEFINE>{+ choice: true false +} DEFINE>{===>} prost_rename_1=false; DEFINE> DEFINE>{* new segid *} DEFINE>{===>} prost_segid_1=""; DEFINE> DEFINE>{* convert chainid to segid if chainid is non-blank *} DEFINE>{+ choice: true false +} DEFINE>{===>} prost_convert_1=true; DEFINE> DEFINE>{============================ ligand files =================================} DEFINE> DEFINE>{* Multiple coordinate files of the same type can be defined by duplicating DEFINE> all of the entries below and incrementing the file number *} DEFINE> DEFINE>{* ligand coordinate file *} DEFINE>{===>} lig_coordinate_infile_1=""; DEFINE> DEFINE>{* rename segid *} DEFINE>{+ choice: true false +} DEFINE>{===>} lig_rename_1=false; DEFINE> DEFINE>{* new segid *} DEFINE>{===>} lig_segid_1=""; DEFINE> DEFINE>{* convert chainid to segid if chainid is non-blank *} DEFINE>{+ choice: true false +} DEFINE>{===>} lig_convert_1=true; DEFINE> DEFINE>{============================== ions files =================================} DEFINE> DEFINE>{* Multiple coordinate files of the same type can be defined by duplicating DEFINE> all of the entries below and incrementing the file number *} DEFINE> DEFINE>{* ion coordinate file *} DEFINE>{===>} ion_coordinate_infile_1=""; DEFINE> DEFINE>{* rename segid *} DEFINE>{+ choice: true false +} DEFINE>{===>} ion_rename_1=false; DEFINE> DEFINE>{* new segid *} DEFINE>{===>} ion_segid_1=""; DEFINE> DEFINE>{* convert chainid to segid if chainid is non-blank *} DEFINE>{+ choice: true false +} DEFINE>{===>} ion_convert_1=true; DEFINE> DEFINE>{============================ renaming atoms ===============================} DEFINE> DEFINE>{* some atoms may need to be renamed in the topology database to conform DEFINE> to what is present in the coordinate file *} DEFINE> DEFINE>{* CNS uses O5 for NDG and A2G carbohydrates. PDB users O. DEFINE> What is it currently called in the coordinate file? *} DEFINE>{* this will not be changed if left blank *} DEFINE>{===>} O5_becomes="O"; DEFINE> DEFINE>{======================= automatic chain breaks ============================} DEFINE> DEFINE>{* automatically detect mainchain breaks in proteins/DNA/RNA based on distance *} DEFINE>{* the link at break points will be removed *} DEFINE>{+ choice: true false +} DEFINE>{===>} auto_break=true; DEFINE> DEFINE>{* cutoff distance in Angstroms for identification of breaks *} DEFINE>{* the default of 2.5A should be reasonable for most cases. If the input DEFINE> structure has bad geometry it may be necessary to increase this distance *} DEFINE>{===>} break_cutoff=2.5; DEFINE> DEFINE>{======================= automatic disulphide bonds ========================} DEFINE> DEFINE>{* automatically detect disulphide bonds based on distance *} DEFINE>{+ choice: true false +} DEFINE>{===>} auto_ss=true; DEFINE> DEFINE>{* cutoff distance in Angstroms for identification of disulphides *} DEFINE>{* the default of 3.0A should be reasonable for most cases. If the input DEFINE> structure has bad geometry it may be necessary to increase this distance *} DEFINE>{* Note: the atom positions for the sulfurs have to be known *} DEFINE>{===>} disulphide_dist=3.0; DEFINE> DEFINE>{========================= manual disulphide bonds =========================} DEFINE> DEFINE>{* Select pairs of cysteine residues that form disulphide bonds *} DEFINE>{* First 2 entries are the segid and resid of the first cysteine (CYS A). *} DEFINE>{* Second 2 entries are the segid and resid of the second cysteine (CYS B). *} DEFINE>{+ table: rows=12 numbered DEFINE> cols=5 "use" "segid CYS A" "resid CYS A" "segid CYS B" "resid CYS B" +} DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_1=false; DEFINE>{===>} ss_i_segid_1=""; ss_i_resid_1=0; DEFINE>{===>} ss_j_segid_1=""; ss_j_resid_1=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_2=false; DEFINE>{===>} ss_i_segid_2=""; ss_i_resid_2=0; DEFINE>{===>} ss_j_segid_2=""; ss_j_resid_2=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_3=false; DEFINE>{===>} ss_i_segid_3=""; ss_i_resid_3=0; DEFINE>{===>} ss_j_segid_3=""; ss_j_resid_3=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_4=false; DEFINE>{===>} ss_i_segid_4=""; ss_i_resid_4=0; DEFINE>{===>} ss_j_segid_4=""; ss_j_resid_4=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_5=false; DEFINE>{===>} ss_i_segid_5=""; ss_i_resid_5=0; DEFINE>{===>} ss_j_segid_5=""; ss_j_resid_5=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_6=false; DEFINE>{===>} ss_i_segid_6=""; ss_i_resid_6=0; DEFINE>{===>} ss_j_segid_6=""; ss_j_resid_6=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_7=false; DEFINE>{===>} ss_i_segid_7=""; ss_i_resid_7=0; DEFINE>{===>} ss_j_segid_7=""; ss_j_resid_7=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_8=false; DEFINE>{===>} ss_i_segid_8=""; ss_i_resid_8=0; DEFINE>{===>} ss_j_segid_8=""; ss_j_resid_8=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_9=false; DEFINE>{===>} ss_i_segid_9=""; ss_i_resid_9=0; DEFINE>{===>} ss_j_segid_9=""; ss_j_resid_9=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_10=false; DEFINE>{===>} ss_i_segid_10=""; ss_i_resid_10=0; DEFINE>{===>} ss_j_segid_10=""; ss_j_resid_10=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_11=false; DEFINE>{===>} ss_i_segid_11=""; ss_i_resid_11=0; DEFINE>{===>} ss_j_segid_11=""; ss_j_resid_11=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} ss_use_12=false; DEFINE>{===>} ss_i_segid_12=""; ss_i_resid_12=0; DEFINE>{===>} ss_j_segid_12=""; ss_j_resid_12=0; DEFINE> DEFINE> DEFINE>{=========================== carbohydrate links ===========================} DEFINE> DEFINE>{* Select pairs of residues that are linked *} DEFINE>{* First entry is the name of the patch residue. *} DEFINE>{* Second and third entries are the resid and segid for the atoms DEFINE> referenced by "-" in the patch. *} DEFINE>{* Fourth and fifth entries are the resid and segid for the atoms DEFINE> referenced by "+" in the patch *} DEFINE>{+ table: rows=20 numbered DEFINE> cols=6 "use" "patch name" "segid -" "resid -" "segid +" "resid +" +} DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_1=false; DEFINE>{===>} carbo_patch_1="B1N"; DEFINE>{===>} carbo_i_segid_1="BBBB"; carbo_i_resid_1=401; DEFINE>{===>} carbo_j_segid_1="AAAA"; carbo_j_resid_1=56; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_2=false; DEFINE>{===>} carbo_patch_2="B1N"; DEFINE>{===>} carbo_i_segid_2="BBBB"; carbo_i_resid_2=402; DEFINE>{===>} carbo_j_segid_2="AAAA"; carbo_j_resid_2=182; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_3=false; DEFINE>{===>} carbo_patch_3=""; DEFINE>{===>} carbo_i_segid_3=""; carbo_i_resid_3=0; DEFINE>{===>} carbo_j_segid_3=""; carbo_j_resid_3=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_4=false; DEFINE>{===>} carbo_patch_4=""; DEFINE>{===>} carbo_i_segid_4=""; carbo_i_resid_4=0; DEFINE>{===>} carbo_j_segid_4=""; carbo_j_resid_4=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_5=false; DEFINE>{===>} carbo_patch_5=""; DEFINE>{===>} carbo_i_segid_5=""; carbo_i_resid_5=0; DEFINE>{===>} carbo_j_segid_5=""; carbo_j_resid_5=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_6=false; DEFINE>{===>} carbo_patch_6=""; DEFINE>{===>} carbo_i_segid_6=""; carbo_i_resid_6=0; DEFINE>{===>} carbo_j_segid_6=""; carbo_j_resid_6=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_7=false; DEFINE>{===>} carbo_patch_7=""; DEFINE>{===>} carbo_i_segid_7=""; carbo_i_resid_7=0; DEFINE>{===>} carbo_j_segid_7=""; carbo_j_resid_7=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_8=false; DEFINE>{===>} carbo_patch_8=""; DEFINE>{===>} carbo_i_segid_8=""; carbo_i_resid_8=0; DEFINE>{===>} carbo_j_segid_8=""; carbo_j_resid_8=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_9=false; DEFINE>{===>} carbo_patch_9=""; DEFINE>{===>} carbo_i_segid_9=""; carbo_i_resid_9=0; DEFINE>{===>} carbo_j_segid_9=""; carbo_j_resid_9=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_10=false; DEFINE>{===>} carbo_patch_10=""; DEFINE>{===>} carbo_i_segid_10=""; carbo_i_resid_10=0; DEFINE>{===>} carbo_j_segid_10=""; carbo_j_resid_10=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_11=false; DEFINE>{===>} carbo_patch_11=""; DEFINE>{===>} carbo_i_segid_11=""; carbo_i_resid_11=0; DEFINE>{===>} carbo_j_segid_11=""; carbo_j_resid_11=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_12=false; DEFINE>{===>} carbo_patch_12=""; DEFINE>{===>} carbo_i_segid_12=""; carbo_i_resid_12=0; DEFINE>{===>} carbo_j_segid_12=""; carbo_j_resid_12=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_13=false; DEFINE>{===>} carbo_patch_13=""; DEFINE>{===>} carbo_i_segid_13=""; carbo_i_resid_13=0; DEFINE>{===>} carbo_j_segid_13=""; carbo_j_resid_13=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_14=false; DEFINE>{===>} carbo_patch_14=""; DEFINE>{===>} carbo_i_segid_14=""; carbo_i_resid_14=0; DEFINE>{===>} carbo_j_segid_14=""; carbo_j_resid_14=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_15=false; DEFINE>{===>} carbo_patch_15=""; DEFINE>{===>} carbo_i_segid_15=""; carbo_i_resid_15=0; DEFINE>{===>} carbo_j_segid_15=""; carbo_j_resid_15=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_16=false; DEFINE>{===>} carbo_patch_16=""; DEFINE>{===>} carbo_i_segid_16=""; carbo_i_resid_16=0; DEFINE>{===>} carbo_j_segid_16=""; carbo_j_resid_16=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_17=false; DEFINE>{===>} carbo_patch_17=""; DEFINE>{===>} carbo_i_segid_17=""; carbo_i_resid_17=0; DEFINE>{===>} carbo_j_segid_17=""; carbo_j_resid_17=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_18=false; DEFINE>{===>} carbo_patch_18=""; DEFINE>{===>} carbo_i_segid_18=""; carbo_i_resid_18=0; DEFINE>{===>} carbo_j_segid_18=""; carbo_j_resid_18=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_19=false; DEFINE>{===>} carbo_patch_19=""; DEFINE>{===>} carbo_i_segid_19=""; carbo_i_resid_19=0; DEFINE>{===>} carbo_j_segid_19=""; carbo_j_resid_19=0; DEFINE> DEFINE>{+ choice: true false +} DEFINE>{===>} carbo_use_20=false; DEFINE>{===>} carbo_patch_20=""; DEFINE>{===>} carbo_i_segid_20=""; carbo_i_resid_20=0; DEFINE>{===>} carbo_j_segid_20=""; carbo_j_resid_20=0; DEFINE> DEFINE>{========================= generate parameters =============================} DEFINE> DEFINE>{* hydrogen flag - determines whether hydrogens will be output *} DEFINE>{* must be true for NMR, atomic resolution X-ray crystallography DEFINE> or modelling. Set to false for X-ray crystallographic DEFINE> applications in the initial stages of refinement. *} DEFINE>{+ choice: true false +} DEFINE>{===>} hydrogen_flag=true; DEFINE> DEFINE>{* selection of atoms to be deleted *} DEFINE>{* to delete all unknown atoms use: (not known) *} DEFINE>{===>} atom_delete=(none); DEFINE> DEFINE>{* selection of atoms for which coordinates will be (re-)generated *} DEFINE>{* to prevent generation of unknown atom use: (none) DEFINE> and set the "selection of atoms to be deleted" to (not known). *} DEFINE>{===>} atom_build=(not known); DEFINE> DEFINE>{* set bfactor flag *} DEFINE>{+ choice: true false +} DEFINE>{===>} set_bfactor=false; DEFINE> DEFINE>{* set bfactor value *} DEFINE>{===>} bfactor=15.0; DEFINE> DEFINE>{* set occupancy flag *} DEFINE>{+ choice: true false +} DEFINE>{===>} set_occupancy=false; DEFINE> DEFINE>{* set occupancy value *} DEFINE>{===>} occupancy=1.0; DEFINE> DEFINE>{============================= output files ================================} DEFINE> DEFINE>{* output structure file *} DEFINE>{===>} structure_outfile="hr64_h2o.mtf"; DEFINE> DEFINE>{* output coordinate file *} DEFINE>{===>} coordinate_outfile="hr64_h2o.pdb"; DEFINE> DEFINE>{===========================================================================} DEFINE>{ things below this line do not need to be changed unless } DEFINE>{ you need to apply patches - at the appropriate places marked } DEFINE>{===========================================================================} DEFINE> DEFINE> ) {- end block parameter definition -} CNSsolve> CNSsolve> checkversion 1.3 Program version= 1.3 File version= 1.3 CNSsolve> CNSsolve> evaluate ($log_level=quiet) Assuming literal string "QUIET" EVALUATE: symbol $LOG_LEVEL set to "QUIET" (string) CNSsolve> CNSsolve> {- read topology files -} CNSsolve> topology RTFRDR> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) RTFRDR> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) RTFRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as true RTFRDR> if ( &exist_topology_infile_$counter = true ) then NEXTCD: condition evaluated as true RTFRDR> if ( &BLANK%topology_infile_$counter = false ) then NEXTCD: condition evaluated as true RTFRDR> @@&topology_infile_$counter ASSFIL: file protein-allhdg5-4.top opened. RTFRDR>remarks file toppar/protein-allhdg5-4.top RTFRDR>remarks RTFRDR>remarks file topallhdg.pro version 5.3 date 23-Sept-02 RTFRDR>remarks for file parallhdg.pro version 5.3 date 13-Feb-02 or later RTFRDR>remarks Geometric energy function parameters for distance geometry and RTFRDR>remarks simulated annealing. RTFRDR>remarks Author: Michael Nilges, EMBL Heidelberg; Institut Pasteur, Paris RTFRDR>remarks This file contains modifications from M. Williams, UCL London RTFRDR>remarks and multiple modifications for HADDOCK from A. Bonvin, Utrecht University RTFRDR>remarks Last modification 30-April-09 RTFRDR> RTFRDR>set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) MESSage=NORM EVALUATE: symbol $OLD_MESSAGE set to "NORM" (string) ECHO=TRUE {ON} EVALUATE: symbol $OLD_ECHO set to TRUE (logical) RTFRDR>set message=off echo=off end %RTFIO-warning: undefined masses in residue HYP %RTFIO error encountered: there are undefined masses. (CNS is in mode: SET ABORT=NORMal END) RTFRDR> end if RTFRDR> else RTFRDR> evaluate ($done=true) RTFRDR> end if RTFRDR> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) RTFRDR> end loop read RTFRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as true RTFRDR> if ( &exist_topology_infile_$counter = true ) then NEXTCD: condition evaluated as true RTFRDR> if ( &BLANK%topology_infile_$counter = false ) then NEXTCD: condition evaluated as true RTFRDR> @@&topology_infile_$counter ASSFIL: file water-allhdg5-4.top opened. RTFRDR>remarks file toppar/water-allhdg5-4.top RTFRDR>remarks RTFRDR>remarks TOPH19.SOL RTFRDR>remarks ========== RTFRDR>remarks topology file for solvent molecules RTFRDR>remarks water models available: TIP3P model RTFRDR> RTFRDR>set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) MESSage=NORM EVALUATE: symbol $OLD_MESSAGE set to "NORM" (string) ECHO=TRUE {ON} EVALUATE: symbol $OLD_ECHO set to TRUE (logical) RTFRDR>set message=off echo=off end RTFRDR> RTFRDR> end if RTFRDR> else RTFRDR> evaluate ($done=true) RTFRDR> end if RTFRDR> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 3.00000 (real) RTFRDR> end loop read RTFRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as true RTFRDR> if ( &exist_topology_infile_$counter = true ) then NEXTCD: condition evaluated as true RTFRDR> if ( &BLANK%topology_infile_$counter = false ) then NEXTCD: condition evaluated as true RTFRDR> @@&topology_infile_$counter ASSFIL: file ion.top opened. RTFRDR>remarks file toppar/ion.top RTFRDR>remarks topology and masses for common ions RTFRDR>remarks Dingle atom ion residues are given the name of the element. RTFRDR>remarks By default the atom will be uncharged (eg. the residue MG will RTFRDR>remarks contain the atom called MG with zero charge). RTFRDR>remarks To use the charged species the charge state is appended to RTFRDR>remarks the atom name (eg to use MG2+ the residue name is MG2, and the RTFRDR>remarks atom name is MG+2 and has charge +2.0). RTFRDR>remarks NOTE: not all ionic species are represented RTFRDR>remarks PDA 02/09/99 RTFRDR> RTFRDR>set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) MESSage=NORM EVALUATE: symbol $OLD_MESSAGE set to "NORM" (string) ECHO=TRUE {ON} EVALUATE: symbol $OLD_ECHO set to TRUE (logical) RTFRDR>set message=off echo=off end %RTFRDR-ERR: duplicate (P-)RESIdue name CO RTFRDR> RTFRDR> end if RTFRDR> else RTFRDR> evaluate ($done=true) RTFRDR> end if RTFRDR> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 4.00000 (real) RTFRDR> end loop read RTFRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as true RTFRDR> if ( &exist_topology_infile_$counter = true ) then NEXTCD: condition evaluated as false RTFRDR> if ( &BLANK%topology_infile_$counter = false ) then RTFRDR> @@&topology_infile_$counter RTFRDR> end if RTFRDR> else RTFRDR> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) RTFRDR> end if RTFRDR> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 5.00000 (real) RTFRDR> end loop read RTFRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as false RTFRDR> if ( &exist_topology_infile_$counter = true ) then RTFRDR> if ( &BLANK%topology_infile_$counter = false ) then RTFRDR> @@&topology_infile_$counter RTFRDR> end if RTFRDR> else RTFRDR> evaluate ($done=true) RTFRDR> end if RTFRDR> evaluate ($counter=$counter+1) RTFRDR> end loop read RTFRDR> end CNSsolve> CNSsolve> do (refy=0) (all) SELRPN: 0 atoms have been selected out of 0 CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop prot NEXTCD: condition evaluated as true CNSsolve> if ( &exist_prot_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%prot_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as true CNSsolve> do (refx=0) (all) SELRPN: 0 atoms have been selected out of 0 CNSsolve> segment SEGMENT> chain CHAIN> if ( &prot_convert_$counter = true ) then NEXTCD: condition evaluated as true CHAIN> convert=true CHAIN> end if CHAIN> if ( &prot_separate_$counter = true ) then NEXTCD: condition evaluated as true CHAIN> separate=true CHAIN> end if CHAIN> evaluate ($count=1) EVALUATE: symbol $COUNT set to 1.00000 (real) CHAIN> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CHAIN> while ( $done = false ) loop read NEXTCD: condition evaluated as true CHAIN> if ( &exist_link_infile_$count = true ) then NEXTCD: condition evaluated as true CHAIN> if ( &BLANK%link_infile_$count = false ) then NEXTCD: condition evaluated as true CHAIN> @@&link_infile_$count ASSFIL: file protein-allhdg5-4.link opened. CHAIN>remarks file toppar/protein-allhdg5-4.link CHAIN>remarks CHAIN>remarks this is a macro to define standard protein peptide bonds CHAIN>remarks and termini to generate a protein sequence. CHAIN> CHAIN>set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) MESSage=NORM EVALUATE: symbol $OLD_MESSAGE set to "NORM" (string) ECHO=TRUE {ON} EVALUATE: symbol $OLD_ECHO set to TRUE (logical) CHAIN>set message=off echo=off end CHAIN> CHAIN> end if CHAIN> else CHAIN> evaluate ($done=true) CHAIN> end if CHAIN> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 2.00000 (real) CHAIN> end loop read CHAIN> while ( $done = false ) loop read NEXTCD: condition evaluated as true CHAIN> if ( &exist_link_infile_$count = true ) then NEXTCD: condition evaluated as true CHAIN> if ( &BLANK%link_infile_$count = false ) then NEXTCD: condition evaluated as false CHAIN> @@&link_infile_$count CHAIN> end if CHAIN> else CHAIN> evaluate ($done=true) CHAIN> end if CHAIN> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 3.00000 (real) CHAIN> end loop read CHAIN> while ( $done = false ) loop read NEXTCD: condition evaluated as true CHAIN> if ( &exist_link_infile_$count = true ) then NEXTCD: condition evaluated as true CHAIN> if ( &BLANK%link_infile_$count = false ) then NEXTCD: condition evaluated as false CHAIN> @@&link_infile_$count CHAIN> end if CHAIN> else CHAIN> evaluate ($done=true) CHAIN> end if CHAIN> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 4.00000 (real) CHAIN> end loop read CHAIN> while ( $done = false ) loop read NEXTCD: condition evaluated as true CHAIN> if ( &exist_link_infile_$count = true ) then NEXTCD: condition evaluated as false CHAIN> if ( &BLANK%link_infile_$count = false ) then CHAIN> @@&link_infile_$count CHAIN> end if CHAIN> else CHAIN> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CHAIN> end if CHAIN> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 5.00000 (real) CHAIN> end loop read CHAIN> while ( $done = false ) loop read NEXTCD: condition evaluated as false CHAIN> if ( &exist_link_infile_$count = true ) then CHAIN> if ( &BLANK%link_infile_$count = false ) then CHAIN> @@&link_infile_$count CHAIN> end if CHAIN> else CHAIN> evaluate ($done=true) CHAIN> end if CHAIN> evaluate ($count=$count+1) CHAIN> end loop read CHAIN> coordinates @@&prot_coordinate_infile_$counter ASSFIL: file template_hr64.pdb opened. COOR>ATOM 1 N MET A 1 1.329 0.000 0.000 1.00 0.00 N SEGMNT-info: chain termination due to END keyword. 69 residues were inserted into segid "A " CHAIN> end SEGMENT> end Status of internal molecular topology database: -> NATOM= 1189(MAXA= 1000000) NBOND= 1205(MAXB= 1000000) -> NTHETA= 2169(MAXT= 2000000) NGRP= 70(MAXGRP= 1000000) -> NPHI= 1800(MAXP= 2000000) NIMPHI= 652(MAXIMP= 1000000) -> NNB= 318(MAXNB= 1000000) CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop prot CNSsolve> while ( $done = false ) loop prot NEXTCD: condition evaluated as false CNSsolve> if ( &exist_prot_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%prot_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &prot_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> if ( &prot_separate_$counter = true ) then CNSsolve> separate=true CNSsolve> end if CNSsolve> evaluate ($count=1) CNSsolve> evaluate ($done=false) CNSsolve> while ( $done = false ) loop read CNSsolve> if ( &exist_link_infile_$count = true ) then CNSsolve> if ( &BLANK%link_infile_$count = false ) then CNSsolve> @@&link_infile_$count CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> evaluate ($count=$count+1) CNSsolve> end loop read CNSsolve> coordinates @@&prot_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop prot CNSsolve> CNSsolve> {- execute custom patches -} CNSsolve> if ( &BLANK%patch_infile = false ) then NEXTCD: condition evaluated as false CNSsolve> display CNSsolve> display executing external patch file CNSsolve> display CNSsolve> inline @&patch_infile CNSsolve> end if CNSsolve> CNSsolve> {* any special protein patches can be applied here *} {* doing it my way (RT) *} CNSsolve> evaluate ($HaveCis = "no") {* --- Apply possible CIS peptide patches --- *} EVALUATE: symbol $HAVECIS set to "no" (string) CNSsolve> if ( $HaveCis = "yes" ) then NEXTCD: condition evaluated as false CNSsolve> !CISpep info CNSsolve> end if CNSsolve> CNSsolve> evaluate ($HaveHisd = "no") {* --- Apply possible HISD peptide patches --- *} EVALUATE: symbol $HAVEHISD set to "no" (string) CNSsolve> if ( $HaveHisd = "yes" ) then NEXTCD: condition evaluated as false CNSsolve> !HISDpep info CNSsolve> end if CNSsolve> CNSsolve> evaluate ($HaveHise = "no") {* --- Apply possible HISE peptide patches --- *} EVALUATE: symbol $HAVEHISE set to "no" (string) CNSsolve> if ( $HaveHise = "yes" ) then NEXTCD: condition evaluated as false CNSsolve> !HISEpep info CNSsolve> end if CNSsolve> CNSsolve> evaluate ($HaveCysn = "no") {* --- Apply possible CYNH peptide patches --- *} EVALUATE: symbol $HAVECYSN set to "no" (string) CNSsolve> if ( $HaveCysn = "yes" ) then NEXTCD: condition evaluated as false CNSsolve> !CYSNpep info CNSsolve> end if CNSsolve> CNSsolve> evaluate ($HaveDisu = "no") {* --- Getting ready for S-S bridges --- *} EVALUATE: symbol $HAVEDISU set to "no" (string) CNSsolve> if ( $HaveDisu = "yes" ) then NEXTCD: condition evaluated as false CNSsolve> !SSBridge info CNSsolve> end if CNSsolve> CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop prot NEXTCD: condition evaluated as true CNSsolve> if ( &exist_prot_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%prot_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as true CNSsolve> coor COOR> if ( &prot_convert_$counter = true ) then NEXTCD: condition evaluated as true COOR> convert=true COOR> end if COOR> @@&prot_coordinate_infile_$counter ASSFIL: file template_hr64.pdb opened. COOR>ATOM 1 N MET A 1 1.329 0.000 0.000 1.00 0.00 N COOR>ATOM 2 CA MET A 1 2.093 -0.001 -1.242 1.00 52.33 C %READC-ERR: atom A 1 MET HN not found in molecular structure %READC-WRN: still 13 missing coordinates (in selected subset) CNSsolve> set echo=off end SELRPN: 0 atoms have been selected out of 1189 SHOW: zero atoms selected NEXTCD: condition evaluated as true %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> if ( &prot_rename_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> do (segid=capitalize(&prot_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop prot CNSsolve> while ( $done = false ) loop prot NEXTCD: condition evaluated as true CNSsolve> if ( &exist_prot_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%prot_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &prot_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&prot_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &prot_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&prot_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop prot CNSsolve> while ( $done = false ) loop prot NEXTCD: condition evaluated as false CNSsolve> if ( &exist_prot_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%prot_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &prot_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&prot_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &prot_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&prot_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop prot CNSsolve> CNSsolve> do (refy=0) (all) SELRPN: 1189 atoms have been selected out of 1189 CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop nucl NEXTCD: condition evaluated as true CNSsolve> if ( &exist_nucl_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%nucl_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &nucl_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> if ( &nucl_separate_$counter = true ) then CNSsolve> separate=true CNSsolve> end if CNSsolve> evaluate ($count=1) CNSsolve> evaluate ($done=false) CNSsolve> while ( $done = false ) loop read CNSsolve> if ( &exist_link_infile_$count = true ) then CNSsolve> if ( &BLANK%link_infile_$count = false ) then CNSsolve> @@&link_infile_$count CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> evaluate ($count=$count+1) CNSsolve> end loop read CNSsolve> coordinates @@&nucl_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &nucl_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop nucl CNSsolve> while ( $done = false ) loop nucl NEXTCD: condition evaluated as true CNSsolve> if ( &exist_nucl_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%nucl_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &nucl_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> if ( &nucl_separate_$counter = true ) then CNSsolve> separate=true CNSsolve> end if CNSsolve> evaluate ($count=1) CNSsolve> evaluate ($done=false) CNSsolve> while ( $done = false ) loop read CNSsolve> if ( &exist_link_infile_$count = true ) then CNSsolve> if ( &BLANK%link_infile_$count = false ) then CNSsolve> @@&link_infile_$count CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> evaluate ($count=$count+1) CNSsolve> end loop read CNSsolve> coordinates @@&nucl_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &nucl_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop nucl CNSsolve> while ( $done = false ) loop nucl NEXTCD: condition evaluated as false CNSsolve> if ( &exist_nucl_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%nucl_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &nucl_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> if ( &nucl_separate_$counter = true ) then CNSsolve> separate=true CNSsolve> end if CNSsolve> evaluate ($count=1) CNSsolve> evaluate ($done=false) CNSsolve> while ( $done = false ) loop read CNSsolve> if ( &exist_link_infile_$count = true ) then CNSsolve> if ( &BLANK%link_infile_$count = false ) then CNSsolve> @@&link_infile_$count CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> evaluate ($count=$count+1) CNSsolve> end loop read CNSsolve> coordinates @@&nucl_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &nucl_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop nucl CNSsolve> CNSsolve> {* any special nucleic acid patches can be applied here *} CNSsolve> {===>} CNSsolve> {<===} CNSsolve> CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop nucl NEXTCD: condition evaluated as true CNSsolve> if ( &exist_nucl_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%nucl_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> coor CNSsolve> if ( &nucl_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&nucl_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &nucl_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&nucl_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop nucl CNSsolve> while ( $done = false ) loop nucl NEXTCD: condition evaluated as true CNSsolve> if ( &exist_nucl_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%nucl_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &nucl_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&nucl_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &nucl_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&nucl_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop nucl CNSsolve> while ( $done = false ) loop nucl NEXTCD: condition evaluated as false CNSsolve> if ( &exist_nucl_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%nucl_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &nucl_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&nucl_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &nucl_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&nucl_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop nucl CNSsolve> CNSsolve>!!! {- patching of RNA to DNA -} CNSsolve>!!! evaluate ($counter=0) CNSsolve>!!! for $id in id ( tag and (&dna_sele) ) loop dna CNSsolve>!!! evaluate ($counter=$counter+1) CNSsolve>!!! show (segid) (id $id) CNSsolve>!!! evaluate ($dna.segid.$counter=$result) CNSsolve>!!! show (resid) (id $id) CNSsolve>!!! evaluate ($dna.resid.$counter=$result) CNSsolve>!!! end loop dna CNSsolve>!!! evaluate ($dna.num=$counter) CNSsolve> CNSsolve>!!! evaluate ($counter=0) CNSsolve>!!! while ($counter < $dna.num) loop dnap CNSsolve>!!! evaluate ($counter=$counter+1) CNSsolve>!!! patch deox reference=nil=(segid $dna.segid.$counter and CNSsolve>!!!! resid $dna.resid.$counter) end CNSsolve>!!! end loop dnap CNSsolve> CNSsolve> if ( $log_level = verbose ) then NEXTCD: condition evaluated as false CNSsolve> set message=normal echo=on end CNSsolve> else CNSsolve> set message=off echo=off end CNSsolve> CNSsolve> CNSsolve> do (refy=0) (all) SELRPN: 1189 atoms have been selected out of 1189 CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop water NEXTCD: condition evaluated as true CNSsolve> if ( &exist_water_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%water_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &water_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&water_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &water_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop water CNSsolve> while ( $done = false ) loop water NEXTCD: condition evaluated as true CNSsolve> if ( &exist_water_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%water_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &water_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&water_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &water_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop water CNSsolve> while ( $done = false ) loop water NEXTCD: condition evaluated as false CNSsolve> if ( &exist_water_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%water_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &water_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&water_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &water_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop water CNSsolve> CNSsolve> {* any special water patches can be applied here *} CNSsolve> {===>} CNSsolve> {<===} CNSsolve> CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop water NEXTCD: condition evaluated as true CNSsolve> if ( &exist_water_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%water_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> coor CNSsolve> if ( &water_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&water_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &water_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&water_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop water CNSsolve> while ( $done = false ) loop water NEXTCD: condition evaluated as true CNSsolve> if ( &exist_water_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%water_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &water_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&water_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &water_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&water_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop water CNSsolve> while ( $done = false ) loop water NEXTCD: condition evaluated as false CNSsolve> if ( &exist_water_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%water_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &water_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&water_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &water_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&water_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop water CNSsolve> CNSsolve> do (refy=0) (all) SELRPN: 1189 atoms have been selected out of 1189 CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop carbo NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%carbo_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &carbo_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&carbo_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &BLANK%O5_becomes = false ) then CNSsolve> do (name=&O5_becomes) (name O5 and ( resname NDG or resname A2G )) CNSsolve> end if CNSsolve> if ( &carbo_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop carbo CNSsolve> while ( $done = false ) loop carbo NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%carbo_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &carbo_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&carbo_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &BLANK%O5_becomes = false ) then CNSsolve> do (name=&O5_becomes) (name O5 and ( resname NDG or resname A2G )) CNSsolve> end if CNSsolve> if ( &carbo_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop carbo CNSsolve> while ( $done = false ) loop carbo NEXTCD: condition evaluated as false CNSsolve> if ( &exist_carbo_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%carbo_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &carbo_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&carbo_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &BLANK%O5_becomes = false ) then CNSsolve> do (name=&O5_becomes) (name O5 and ( resname NDG or resname A2G )) CNSsolve> end if CNSsolve> if ( &carbo_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop carbo CNSsolve> CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop carbo NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%carbo_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> coor CNSsolve> if ( &carbo_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&carbo_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &carbo_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&carbo_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop carbo CNSsolve> while ( $done = false ) loop carbo NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%carbo_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &carbo_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&carbo_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &carbo_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&carbo_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop carbo CNSsolve> while ( $done = false ) loop carbo NEXTCD: condition evaluated as false CNSsolve> if ( &exist_carbo_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%carbo_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &carbo_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&carbo_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &carbo_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&carbo_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop carbo CNSsolve> CNSsolve> evaluate ($carc=1) EVALUATE: symbol $CARC set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 3.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 4.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 5.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 6.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 7.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 8.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 9.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 10.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 11.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 12.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 13.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 14.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 15.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 16.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 17.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 18.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 19.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 20.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) EVALUATE: symbol $CARC set to 21.0000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as true CNSsolve> if ( &exist_carbo_use_$carc = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &carbo_use_$carc = true ) then CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> while ( $done = false ) loop cabr NEXTCD: condition evaluated as false CNSsolve> if ( &exist_carbo_use_$carc = true ) then CNSsolve> if ( &carbo_use_$carc = true ) then CNSsolve> evaluate ($segidtmp1=capitalize(&carbo_i_segid_$carc)) CNSsolve> evaluate ($segidtmp2=capitalize(&carbo_j_segid_$carc)) CNSsolve> patch &carbo_patch_$carc CNSsolve> reference=-=(segid $QUOTE%segidtmp1 and CNSsolve> resid &carbo_i_resid_$carc) CNSsolve> reference=+=(segid $QUOTE%segidtmp2 and CNSsolve> resid &carbo_j_resid_$carc) CNSsolve> end CNSsolve> end if CNSsolve> evaluate ($carc=$carc+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop cabr CNSsolve> CNSsolve> {* any special carbohydrate patches can be applied here *} CNSsolve> {===>} CNSsolve> {<===} CNSsolve> CNSsolve> do (refy=0) (all) SELRPN: 1189 atoms have been selected out of 1189 CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop prost NEXTCD: condition evaluated as true CNSsolve> if ( &exist_prost_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%prost_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &prost_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&prost_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &prost_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop prost CNSsolve> while ( $done = false ) loop prost NEXTCD: condition evaluated as true CNSsolve> if ( &exist_prost_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%prost_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &prost_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&prost_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &prost_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop prost CNSsolve> while ( $done = false ) loop prost NEXTCD: condition evaluated as false CNSsolve> if ( &exist_prost_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%prost_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &prost_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&prost_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &prost_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop prost CNSsolve> CNSsolve> {* any special prosthetic group patches can be applied here *} CNSsolve> {===>} CNSsolve> {<===} CNSsolve> CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop prost NEXTCD: condition evaluated as true CNSsolve> if ( &exist_prost_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%prost_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> coor CNSsolve> if ( &prost_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&prost_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &prost_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&prost_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop prost CNSsolve> while ( $done = false ) loop prost NEXTCD: condition evaluated as true CNSsolve> if ( &exist_prost_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%prost_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &prost_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&prost_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &prost_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&prost_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop prost CNSsolve> while ( $done = false ) loop prost NEXTCD: condition evaluated as false CNSsolve> if ( &exist_prost_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%prost_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &prost_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&prost_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &prost_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&prost_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop prost CNSsolve> CNSsolve> do (refy=0) (all) SELRPN: 1189 atoms have been selected out of 1189 CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop liga NEXTCD: condition evaluated as true CNSsolve> if ( &exist_lig_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%lig_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &lig_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&lig_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &lig_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop liga CNSsolve> while ( $done = false ) loop liga NEXTCD: condition evaluated as true CNSsolve> if ( &exist_lig_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%lig_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &lig_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&lig_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &lig_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop liga CNSsolve> while ( $done = false ) loop liga NEXTCD: condition evaluated as false CNSsolve> if ( &exist_lig_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%lig_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &lig_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&lig_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &lig_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop liga CNSsolve> CNSsolve> {* any special ligand patches can be applied here *} CNSsolve> {===>} CNSsolve> {<===} CNSsolve> CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop liga NEXTCD: condition evaluated as true CNSsolve> if ( &exist_lig_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%lig_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> coor CNSsolve> if ( &lig_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&lig_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &lig_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&lig_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop liga CNSsolve> while ( $done = false ) loop liga NEXTCD: condition evaluated as true CNSsolve> if ( &exist_lig_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%lig_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &lig_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&lig_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &lig_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&lig_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop liga CNSsolve> while ( $done = false ) loop liga NEXTCD: condition evaluated as false CNSsolve> if ( &exist_lig_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%lig_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &lig_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&lig_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &lig_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&lig_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop liga CNSsolve> CNSsolve> do (refy=0) (all) SELRPN: 1189 atoms have been selected out of 1189 CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop ion NEXTCD: condition evaluated as true CNSsolve> if ( &exist_ion_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%ion_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &ion_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&ion_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &ion_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop ion CNSsolve> while ( $done = false ) loop ion NEXTCD: condition evaluated as true CNSsolve> if ( &exist_ion_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%ion_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &ion_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&ion_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &ion_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop ion CNSsolve> while ( $done = false ) loop ion NEXTCD: condition evaluated as false CNSsolve> if ( &exist_ion_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%ion_coordinate_infile_$counter = false ) then CNSsolve> do (refx=0) (all) CNSsolve> segment CNSsolve> chain CNSsolve> if ( &ion_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> coordinates @@&ion_coordinate_infile_$counter CNSsolve> end CNSsolve> end CNSsolve> if ( &ion_rename_$counter = true ) then CNSsolve> do (refy=$counter) (attr refx=9999) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop ion CNSsolve> CNSsolve> {* any special ion patches can be applied here *} CNSsolve> {===>} CNSsolve> {<===} CNSsolve> CNSsolve> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop ion NEXTCD: condition evaluated as true CNSsolve> if ( &exist_ion_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%ion_coordinate_infile_$counter = false ) then NEXTCD: condition evaluated as false CNSsolve> coor CNSsolve> if ( &ion_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&ion_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &ion_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&ion_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop ion CNSsolve> while ( $done = false ) loop ion NEXTCD: condition evaluated as true CNSsolve> if ( &exist_ion_coordinate_infile_$counter = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%ion_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &ion_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&ion_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &ion_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&ion_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> end if CNSsolve> end loop ion CNSsolve> while ( $done = false ) loop ion NEXTCD: condition evaluated as false CNSsolve> if ( &exist_ion_coordinate_infile_$counter = true ) then CNSsolve> if ( &BLANK%ion_coordinate_infile_$counter = false ) then CNSsolve> coor CNSsolve> if ( &ion_convert_$counter = true ) then CNSsolve> convert=true CNSsolve> end if CNSsolve> @@&ion_coordinate_infile_$counter CNSsolve> set echo=off end CNSsolve> show sum(1) ( not(hydrogen) and not(known) ) CNSsolve> if ( $select = 0 ) then CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms CNSsolve> end if CNSsolve> set echo=on end CNSsolve> if ( &ion_rename_$counter = true ) then CNSsolve> do (segid=capitalize(&ion_segid_$counter)) (attr refy=$counter) CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($counter=$counter+1) CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> end if CNSsolve> end loop ion CNSsolve> CNSsolve> CNSsolve> {* any final patches can be applied here *} CNSsolve> {===>} CNSsolve> {<===} CNSsolve> CNSsolve> if (&hydrogen_flag=false) then NEXTCD: condition evaluated as false CNSsolve> delete selection=( hydrogen ) end CNSsolve> end if CNSsolve> CNSsolve> delete selection=( &atom_delete ) end SELRPN: 0 atoms have been selected out of 1189 SCRATC-warning: STORe selections erased. Status of internal molecular topology database: -> NATOM= 1189(MAXA= 1000000) NBOND= 1205(MAXB= 1000000) -> NTHETA= 2169(MAXT= 2000000) NGRP= 70(MAXGRP= 1000000) -> NPHI= 1800(MAXP= 2000000) NIMPHI= 652(MAXIMP= 1000000) -> NNB= 318(MAXNB= 1000000) CNSsolve> CNSsolve> {- read parameter files -} CNSsolve> {- here atom-based parameter files are possible as well since all atoms have been defined -} CNSsolve> parameter PARRDR> evaluate ($counter=1) EVALUATE: symbol $COUNTER set to 1.00000 (real) PARRDR> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) PARRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as true PARRDR> if ( &exist_parameter_infile_$counter = true ) then NEXTCD: condition evaluated as true PARRDR> if ( &BLANK%parameter_infile_$counter = false ) then NEXTCD: condition evaluated as true PARRDR> @@¶meter_infile_$counter ASSFIL: file protein-allhdg5-4.param opened. PARRDR>remarks file toppar/protein-allhdg5-4.param PARRDR>remarks PARRDR>remarks file protein-allhdg-ucl.param version UCL date 07-JUL-01 PARRDR>remarks for file protein-allhdg-ucl.top version UCL date 14-MAR-00 PARRDR>remarks for file protein-allhdg-dih-ucl.top version UCL date 07-JUL-01 PARRDR>remarks Geometric energy function parameters for distance geometry and PARRDR>remarks simulated annealing. PARRDR>remarks Original author: Michael Nilges, EMBL Heidelberg PARRDR>remarks Modifications: Mark A. Williams, UCL London PARRDR> PARRDR>set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) MESSage=NORM EVALUATE: symbol $OLD_MESSAGE set to "NORM" (string) ECHO=TRUE {ON} EVALUATE: symbol $OLD_ECHO set to TRUE (logical) PARRDR>set message=off echo=off end PARRDR> PARRDR> end if PARRDR> else PARRDR> evaluate ($done=true) PARRDR> end if PARRDR> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 2.00000 (real) PARRDR> end loop read PARRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as true PARRDR> if ( &exist_parameter_infile_$counter = true ) then NEXTCD: condition evaluated as true PARRDR> if ( &BLANK%parameter_infile_$counter = false ) then NEXTCD: condition evaluated as true PARRDR> @@¶meter_infile_$counter ASSFIL: file water-allhdg5-4.param opened. PARRDR>remarks file toppar/water-allhdg5-4.param PARRDR>remarks PARRDR>remarks PARAM19.SOL (solvent parameters) PARRDR>remarks =========== PARRDR>remarks available: TIPS3P and DMSO model PARRDR> PARRDR>set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) MESSage=NORM EVALUATE: symbol $OLD_MESSAGE set to "NORM" (string) ECHO=TRUE {ON} EVALUATE: symbol $OLD_ECHO set to TRUE (logical) PARRDR>set message=off echo=off end PARRDR> end if PARRDR> else PARRDR> evaluate ($done=true) PARRDR> end if PARRDR> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 3.00000 (real) PARRDR> end loop read PARRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as true PARRDR> if ( &exist_parameter_infile_$counter = true ) then NEXTCD: condition evaluated as true PARRDR> if ( &BLANK%parameter_infile_$counter = false ) then NEXTCD: condition evaluated as true PARRDR> @@¶meter_infile_$counter ASSFIL: file ion.param opened. PARRDR>remarks file toppar/ion.param PARRDR>remarks nonbonded parameters for common ions PARRDR>remarks new parameters derived from literature for single atom species PARRDR>remarks PDA 02/09/99 PARRDR> PARRDR>set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) MESSage=NORM EVALUATE: symbol $OLD_MESSAGE set to "NORM" (string) ECHO=TRUE {ON} EVALUATE: symbol $OLD_ECHO set to TRUE (logical) PARRDR>set message=off echo=off end PARRDR> PARRDR> end if PARRDR> else PARRDR> evaluate ($done=true) PARRDR> end if PARRDR> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 4.00000 (real) PARRDR> end loop read PARRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as true PARRDR> if ( &exist_parameter_infile_$counter = true ) then NEXTCD: condition evaluated as false PARRDR> if ( &BLANK%parameter_infile_$counter = false ) then PARRDR> @@¶meter_infile_$counter PARRDR> end if PARRDR> else PARRDR> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) PARRDR> end if PARRDR> evaluate ($counter=$counter+1) EVALUATE: symbol $COUNTER set to 5.00000 (real) PARRDR> end loop read PARRDR> while ( $done = false ) loop read NEXTCD: condition evaluated as false PARRDR> if ( &exist_parameter_infile_$counter = true ) then PARRDR> if ( &BLANK%parameter_infile_$counter = false ) then PARRDR> @@¶meter_infile_$counter PARRDR> end if PARRDR> else PARRDR> evaluate ($done=true) PARRDR> end if PARRDR> evaluate ($counter=$counter+1) PARRDR> end loop read PARRDR> end %PARRDR-ERROR: duplication of bond HC NC2 %PARRDR-ERROR: duplication of bond OUF SUF %PARRDR-ERROR: duplication of angle CH2P CH2E HA %PARRDR-ERROR: duplication of angle OUF SUF OUF %PARRDR-ERROR: duplication of nonbonded entry OS %PARRDR-ERROR: duplication of nonbonded entry SUF %PARRDR-ERROR: duplication of nonbonded entry OUF CNSsolve> CNSsolve> {- build atoms if requested -} CNSsolve> identity (store1) (&atom_build) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> show sum(1) (store1) SELRPN: 13 atoms have been selected out of 1189 SHOW: sum over selected elements = 13.000000 CNSsolve> evaluate ($tobuild=$result) EVALUATE: symbol $TOBUILD set to 13.0000 (real) CNSsolve> CNSsolve> if ( $tobuild > 0 ) then NEXTCD: condition evaluated as true CNSsolve> CNSsolve> fix selection=(not(store1)) end SELRPN: 1176 atoms have been selected out of 1189 CNSsolve> CNSsolve> for $id in id (tag and byres(store1)) loop avco SELRPN: 11 atoms have been selected out of 1189 FOR ID LOOP: symbol ID set to 1.00000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 16 atoms have been selected out of 1189 SHOW: average of selected elements = 3.865938 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to 3.86594 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 16 atoms have been selected out of 1189 SHOW: average of selected elements = 0.513125 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to 0.513125 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 16 atoms have been selected out of 1189 SHOW: average of selected elements = -2.049500 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to -2.04950 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 3 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 3 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 3 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 27.0000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -4.658471 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -4.65847 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -1.007118 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -1.00712 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -3.685941 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to -3.68594 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 45.0000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -4.809941 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -4.80994 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -6.644294 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -6.64429 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -4.351706 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to -4.35171 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 63.0000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -10.756118 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -10.7561 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -5.421059 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -5.42106 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -7.277118 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to -7.27712 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 81.0000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -11.688882 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -11.6889 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -10.748882 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -10.7489 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -5.416353 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to -5.41635 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 99.0000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -15.683294 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -15.6833 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -10.812824 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -10.8128 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -7.611294 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to -7.61129 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 117.000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -17.817235 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -17.8172 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -10.170765 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -10.1708 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -1.707588 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to -1.70759 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 146.000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -24.389471 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -24.3895 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -8.024235 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -8.02424 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -2.504059 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to -2.50406 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 192.000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -32.872588 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -32.8726 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -4.965706 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -4.96571 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = 1.478588 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to 1.47859 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 402.000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -32.783059 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -32.7831 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -11.460824 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -11.4608 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = 19.781235 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to 19.7812 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco FOR ID LOOP: symbol ID set to 583.000 (real) CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -33.098294 CNSsolve> evaluate ($ave_x=$result) EVALUATE: symbol $AVE_X set to -33.0983 (real) CNSsolve> show ave(y) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = -22.995176 CNSsolve> evaluate ($ave_y=$result) EVALUATE: symbol $AVE_Y set to -22.9952 (real) CNSsolve> show ave(z) (byres(id $id) and known) SELRPN: 17 atoms have been selected out of 1189 SHOW: average of selected elements = 12.035529 CNSsolve> evaluate ($ave_z=$result) EVALUATE: symbol $AVE_Z set to 12.0355 (real) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (y=$ave_y) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> do (z=$ave_z) (byres(id $id) and store1) SELRPN: 1 atoms have been selected out of 1189 CNSsolve> CNSsolve> end loop avco CNSsolve> for $id in id (tag and byres(store1)) loop avco CNSsolve> CNSsolve> show ave(x) (byres(id $id) and known) CNSsolve> evaluate ($ave_x=$result) CNSsolve> show ave(y) (byres(id $id) and known) CNSsolve> evaluate ($ave_y=$result) CNSsolve> show ave(z) (byres(id $id) and known) CNSsolve> evaluate ($ave_z=$result) CNSsolve> CNSsolve> do (x=$ave_x) (byres(id $id) and store1) CNSsolve> do (y=$ave_y) (byres(id $id) and store1) CNSsolve> do (z=$ave_z) (byres(id $id) and store1) CNSsolve> CNSsolve> end loop avco CNSsolve> CNSsolve> do (x=x+random(2.0)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (y=y+random(2.0)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (z=z+random(2.0)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> {- start parameter for the side chain building -} CNSsolve> parameter PARRDR> nbonds NBDSET> rcon=20. nbxmod=-2 repel=0.9 wmin=0.1 tolerance=1. NBDSET> rexp=2 irexp=2 inhibit=0.25 NBDSET> end PARRDR> end %PARRDR-ERROR: duplication of bond HC NC2 %PARRDR-ERROR: duplication of bond OUF SUF %PARRDR-ERROR: duplication of angle CH2P CH2E HA %PARRDR-ERROR: duplication of angle OUF SUF OUF %PARRDR-ERROR: duplication of nonbonded entry OS %PARRDR-ERROR: duplication of nonbonded entry SUF %PARRDR-ERROR: duplication of nonbonded entry OUF CNSsolve> CNSsolve> {- Friction coefficient, in 1/ps. -} CNSsolve> do (fbeta=100) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> evaluate ($bath=300.0) EVALUATE: symbol $BATH set to 300.000 (real) CNSsolve> evaluate ($nstep=500) EVALUATE: symbol $NSTEP set to 500.000 (real) CNSsolve> evaluate ($timestep=0.0005) EVALUATE: symbol $TIMESTEP set to 0.500000E-03 (real) CNSsolve> CNSsolve> do (refy=mass) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> do (mass=20) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> igroup interaction SELRPN> (store1) (store1 or known) SELRPN: 13 atoms have been selected out of 1189 SELRPN: 1189 atoms have been selected out of 1189 IGROup> end CNSsolve> CNSsolve> {- turn on initial energy terms -} CNSsolve> flags exclude * include bond angle vdw end CNSsolve> CNSsolve> minimize lbfgs nstep=50 nprint=10 end LBFGS: number of degrees of freedom= 39 NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 13 exclusions and 0 interactions(1-4) NBONDS: found 920 intra-atom interactions NBONDS: found 769 intra-atom interactions NBONDS: found 644 intra-atom interactions NBONDS: found 689 intra-atom interactions NBONDS: found 677 intra-atom interactions ------------------------------ cycle= 10 ----------------------------------- | Etotal =2012.338 grad(E)=42.825 E(BOND)=806.527 E(ANGL)=41.599 | | E(VDW )=1164.211 | ------------------------------------------------------------------------------- NBONDS: found 678 intra-atom interactions ------------------------------ cycle= 20 ----------------------------------- | Etotal =1957.728 grad(E)=40.951 E(BOND)=695.231 E(ANGL)=40.240 | | E(VDW )=1222.257 | ------------------------------------------------------------------------------- ------------------------------ cycle= 30 ----------------------------------- | Etotal =1957.728 grad(E)=40.953 E(BOND)=695.153 E(ANGL)=40.275 | | E(VDW )=1222.300 | ------------------------------------------------------------------------------- ------------------------------ cycle= 40 ----------------------------------- | Etotal =1957.728 grad(E)=40.953 E(BOND)=695.154 E(ANGL)=40.275 | | E(VDW )=1222.299 | ------------------------------------------------------------------------------- LBFGS: normal termination - gradient converged CNSsolve> CNSsolve> do (vx=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (vy=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (vz=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> flags exclude vdw include impr end CNSsolve> CNSsolve> dynamics cartesian Cartesian Dynamics> nstep=50 Cartesian Dynamics> timestep=$timestep Cartesian Dynamics> tcoupling=true temperature=$bath DCART: temperature coupling (TCOUpling) enabled Cartesian Dynamics> nprint=$nstep Cartesian Dynamics> cmremove=false Cartesian Dynamics> end -------------------------- Cartesian dynamics start --------------------------- | E(kin)+E(total)=3437.934 E(kin)=11.824 temperature=305.123 | | Etotal =3426.111 grad(E)=56.503 E(BOND)=695.154 E(ANGL)=40.275 | | E(IMPR)=2690.682 | ------------------------------------------------------------------------------- ----------------- final step= 50 at 0.02500 ps --------------------- | E(kin)+E(total)=2389.951 E(kin)=275.808 temperature=7117.597 | | Etotal =2114.143 grad(E)=20.280 E(BOND)=25.105 E(ANGL)=652.324 | | E(IMPR)=1436.714 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -14.84773 -6.83989 0.35817 velocity [A/ps] : -0.16841 1.17197 -1.89238 ang. mom. [amu A/ps] : -17776.42782 452.27857 -35177.30077 kin. ener. [Kcal/mol] : 1.54824 CNSsolve> CNSsolve> flags include vdw end CNSsolve> CNSsolve> minimize lbfgs nstep=50 nprint=10 end LBFGS: number of degrees of freedom= 39 NBONDS: found 678 intra-atom interactions NBONDS: found 669 intra-atom interactions ------------------------------ cycle= 10 ----------------------------------- | Etotal =1959.041 grad(E)=40.688 E(BOND)=701.322 E(ANGL)=33.503 | | E(IMPR)=0.155 E(VDW )=1224.061 | ------------------------------------------------------------------------------- ------------------------------ cycle= 20 ----------------------------------- | Etotal =1957.728 grad(E)=40.954 E(BOND)=695.150 E(ANGL)=40.286 | | E(IMPR)=0.000 E(VDW )=1222.292 | ------------------------------------------------------------------------------- ------------------------------ cycle= 30 ----------------------------------- | Etotal =1957.728 grad(E)=40.953 E(BOND)=695.143 E(ANGL)=40.286 | | E(IMPR)=0.000 E(VDW )=1222.299 | ------------------------------------------------------------------------------- LBFGS: normal termination - gradient converged CNSsolve> CNSsolve> do (vx=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (vy=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (vz=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> dynamics cartesian Cartesian Dynamics> nstep=50 Cartesian Dynamics> timestep=$timestep Cartesian Dynamics> tcoupling=true temperature=$bath DCART: temperature coupling (TCOUpling) enabled Cartesian Dynamics> nprint=$nstep Cartesian Dynamics> cmremove=false Cartesian Dynamics> end -------------------------- Cartesian dynamics start --------------------------- | E(kin)+E(total)=1971.414 E(kin)=13.687 temperature=353.200 | | Etotal =1957.728 grad(E)=40.953 E(BOND)=695.143 E(ANGL)=40.286 | | E(IMPR)=0.000 E(VDW )=1222.299 | ------------------------------------------------------------------------------- ----------------- final step= 50 at 0.02500 ps --------------------- | E(kin)+E(total)=1977.483 E(kin)=9.419 temperature=243.065 | | Etotal =1968.065 grad(E)=41.510 E(BOND)=689.423 E(ANGL)=50.306 | | E(IMPR)=0.004 E(VDW )=1228.332 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -14.84303 -6.77783 0.39531 velocity [A/ps] : 1.05614 -0.36205 0.16530 ang. mom. [amu A/ps] : 1856.74062 635.53498 -616.04698 kin. ener. [Kcal/mol] : 0.39579 CNSsolve> CNSsolve> parameter PARRDR> nbonds NBDSET> rcon=2. nbxmod=-3 repel=0.75 NBDSET> end PARRDR> end %PARRDR-ERROR: duplication of bond HC NC2 %PARRDR-ERROR: duplication of bond OUF SUF %PARRDR-ERROR: duplication of angle CH2P CH2E HA %PARRDR-ERROR: duplication of angle OUF SUF OUF %PARRDR-ERROR: duplication of nonbonded entry OS %PARRDR-ERROR: duplication of nonbonded entry SUF %PARRDR-ERROR: duplication of nonbonded entry OUF CNSsolve> CNSsolve> minimize lbfgs nstep=100 nprint=25 end LBFGS: number of degrees of freedom= 39 NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 39 exclusions and 0 interactions(1-4) NBONDS: found 641 intra-atom interactions ------------------------------ cycle= 25 ----------------------------------- | Etotal =0.382 grad(E)=0.108 E(BOND)=0.000 E(ANGL)=0.381 | | E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- ------------------------------ cycle= 50 ----------------------------------- | Etotal =0.369 grad(E)=0.033 E(BOND)=0.000 E(ANGL)=0.368 | | E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- ------------------------------ cycle= 75 ----------------------------------- | Etotal =0.367 grad(E)=0.002 E(BOND)=0.000 E(ANGL)=0.367 | | E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- ------------------------------ cycle= 100 ----------------------------------- | Etotal =0.367 grad(E)=0.002 E(BOND)=0.000 E(ANGL)=0.367 | | E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- LBFGS: normal termination - NSTEP limit reached CNSsolve> CNSsolve> do (vx=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (vy=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (vz=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> dynamics cartesian Cartesian Dynamics> nstep=$nstep Cartesian Dynamics> timestep=$timestep Cartesian Dynamics> tcoupling=true temperature=$bath DCART: temperature coupling (TCOUpling) enabled Cartesian Dynamics> nprint=$nstep Cartesian Dynamics> cmremove=false Cartesian Dynamics> end -------------------------- Cartesian dynamics start --------------------------- | E(kin)+E(total)=16.173 E(kin)=15.806 temperature=407.892 | | Etotal =0.367 grad(E)=0.002 E(BOND)=0.000 E(ANGL)=0.367 | | E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- NBONDS: found 655 intra-atom interactions ----------------- final step= 500 at 0.25000 ps --------------------- | E(kin)+E(total)=18.535 E(kin)=10.951 temperature=282.607 | | Etotal =7.584 grad(E)=3.603 E(BOND)=1.260 E(ANGL)=6.304 | | E(IMPR)=0.020 E(VDW )=0.000 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -14.82582 -6.81885 0.31011 velocity [A/ps] : 1.21871 -1.86489 -0.43149 ang. mom. [amu A/ps] : 531.03292 4349.59043 4984.73655 kin. ener. [Kcal/mol] : 1.59992 CNSsolve> CNSsolve> {- turn on all energy terms -} CNSsolve> flags include dihe ? end EFLAGS: the following energy flags are set EFLAGS: BOND ANGL DIHE IMPR VDW CNSsolve> CNSsolve> {- set repel to ~vdw radii -} CNSsolve> parameter PARRDR> nbonds NBDSET> repel=0.89 NBDSET> end PARRDR> end %PARRDR-ERROR: duplication of bond HC NC2 %PARRDR-ERROR: duplication of bond OUF SUF %PARRDR-ERROR: duplication of angle CH2P CH2E HA %PARRDR-ERROR: duplication of angle OUF SUF OUF %PARRDR-ERROR: duplication of nonbonded entry OS %PARRDR-ERROR: duplication of nonbonded entry SUF %PARRDR-ERROR: duplication of nonbonded entry OUF CNSsolve> CNSsolve> minimize lbfgs nstep=500 nprint=50 end LBFGS: number of degrees of freedom= 39 NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 39 exclusions and 0 interactions(1-4) NBONDS: found 658 intra-atom interactions ------------------------------ cycle= 50 ----------------------------------- | Etotal =0.385 grad(E)=0.116 E(BOND)=0.000 E(ANGL)=0.385 | | E(DIHE)=0.000 E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- ------------------------------ cycle= 100 ----------------------------------- | Etotal =0.367 grad(E)=0.009 E(BOND)=0.000 E(ANGL)=0.367 | | E(DIHE)=0.000 E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- ------------------------------ cycle= 150 ----------------------------------- | Etotal =0.367 grad(E)=0.002 E(BOND)=0.000 E(ANGL)=0.367 | | E(DIHE)=0.000 E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- LBFGS: normal termination - gradient converged CNSsolve> CNSsolve> flags exclude * include bond angl impr dihe vdw end CNSsolve> CNSsolve> {- return masses to something sensible -} CNSsolve> do (mass=refy) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> do (vx=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (vy=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> do (vz=maxwell($bath)) (store1) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> CNSsolve> dynamics cartesian Cartesian Dynamics> nstep=$nstep Cartesian Dynamics> timestep=$timestep Cartesian Dynamics> tcoupling=true temperature=$bath DCART: temperature coupling (TCOUpling) enabled Cartesian Dynamics> nprint=$nstep Cartesian Dynamics> cmremove=false Cartesian Dynamics> end -------------------------- Cartesian dynamics start --------------------------- | E(kin)+E(total)=12.750 E(kin)=12.383 temperature=319.554 | | Etotal =0.367 grad(E)=0.002 E(BOND)=0.000 E(ANGL)=0.367 | | E(DIHE)=0.000 E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- ----------------- final step= 500 at 0.25000 ps --------------------- | E(kin)+E(total)=20.319 E(kin)=13.051 temperature=336.794 | | Etotal =7.268 grad(E)=3.710 E(BOND)=1.437 E(ANGL)=5.816 | | E(DIHE)=0.000 E(IMPR)=0.015 E(VDW )=0.000 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -14.77133 -6.80718 0.32334 velocity [A/ps] : -3.03352 -0.70406 -1.74671 ang. mom. [amu A/ps] : 171.16482 -383.85833 1515.70704 kin. ener. [Kcal/mol] : 0.19964 CNSsolve> CNSsolve> {- some final minimisation -} CNSsolve> minimize lbfgs LBFGS> nstep=500 LBFGS> drop=40.0 LBFGS> nprint=50 LBFGS> end LBFGS: number of degrees of freedom= 39 ------------------------------ cycle= 50 ----------------------------------- | Etotal =0.367 grad(E)=0.002 E(BOND)=0.000 E(ANGL)=0.367 | | E(DIHE)=0.000 E(IMPR)=0.000 E(VDW )=0.000 | ------------------------------------------------------------------------------- LBFGS: normal termination - gradient converged CNSsolve> CNSsolve> print thres=0.02 bonds (atom-i |atom-j ) dist. equil. delta energy const. Number of violations greater 0.020: 0 RMS deviation= 0.000 CNSsolve> print thres=5. angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. Number of violations greater 5.000: 0 RMS deviation= 0.304 CNSsolve> CNSsolve> fix selection=( none ) end SELRPN: 0 atoms have been selected out of 1189 CNSsolve> CNSsolve> end if CNSsolve> CNSsolve> set echo=false end SELRPN: 0 atoms have been selected out of 1189 SHOW: zero atoms selected NEXTCD: condition evaluated as true SELRPN: 0 atoms have been selected out of 1189 CNSsolve> CNSsolve> if (&set_bfactor=true) then NEXTCD: condition evaluated as false CNSsolve> do (b=&bfactor) ( all ) CNSsolve> else CNSsolve> show ave(b) (known and not(store1)) SELRPN: 1176 atoms have been selected out of 1189 SHOW: average of selected elements = 38.193707 CNSsolve> do (b=$result) (store1 and (attr b < 0.01)) SELRPN: 13 atoms have been selected out of 1189 CNSsolve> end if CNSsolve> CNSsolve> if (&set_occupancy=true) then NEXTCD: condition evaluated as false CNSsolve> do (q=&occupancy) ( all ) CNSsolve> end if CNSsolve> CNSsolve> set echo=false end SELRPN: 13 atoms have been selected out of 1189 SHOW: sum over selected elements = 13.000000 NEXTCD: condition evaluated as true SELRPN: 13 atoms have been selected out of 1189 FOR ID LOOP: symbol ID set to 16.0000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT1 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT1 ) MET EVALUATE: symbol $RESNAME set to "MET" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT1 ) 1 EVALUATE: symbol $RESID set to "1" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT1 ) HT1 EVALUATE: symbol $NAME set to "HT1" (string) FOR ID LOOP: symbol ID set to 17.0000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT2 ) MET EVALUATE: symbol $RESNAME set to "MET" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT2 ) 1 EVALUATE: symbol $RESID set to "1" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT2 ) HT2 EVALUATE: symbol $NAME set to "HT2" (string) FOR ID LOOP: symbol ID set to 18.0000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT3 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT3 ) MET EVALUATE: symbol $RESNAME set to "MET" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT3 ) 1 EVALUATE: symbol $RESID set to "1" (string) SELRPN: 1 atoms have been selected out of 1189 ( A MET 1 HT3 ) HT3 EVALUATE: symbol $NAME set to "HT3" (string) FOR ID LOOP: symbol ID set to 42.0000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 3 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 3 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 3 HE2 ) 3 EVALUATE: symbol $RESID set to "3" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 3 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 60.0000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 4 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 4 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 4 HE2 ) 4 EVALUATE: symbol $RESID set to "4" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 4 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 78.0000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 5 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 5 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 5 HE2 ) 5 EVALUATE: symbol $RESID set to "5" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 5 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 96.0000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 6 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 6 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 6 HE2 ) 6 EVALUATE: symbol $RESID set to "6" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 6 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 114.000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 7 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 7 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 7 HE2 ) 7 EVALUATE: symbol $RESID set to "7" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 7 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 132.000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 8 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 8 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 8 HE2 ) 8 EVALUATE: symbol $RESID set to "8" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 8 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 161.000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 10 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 10 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 10 HE2 ) 10 EVALUATE: symbol $RESID set to "10" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 10 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 207.000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 13 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 13 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 13 HE2 ) 13 EVALUATE: symbol $RESID set to "13" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 13 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 417.000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 25 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 25 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 25 HE2 ) 25 EVALUATE: symbol $RESID set to "25" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 25 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) FOR ID LOOP: symbol ID set to 598.000 (real) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 36 HE2 ) A EVALUATE: symbol $SEGID set to "A" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 36 HE2 ) HIS EVALUATE: symbol $RESNAME set to "HIS" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 36 HE2 ) 36 EVALUATE: symbol $RESID set to "36" (string) SELRPN: 1 atoms have been selected out of 1189 ( A HIS 36 HE2 ) HE2 EVALUATE: symbol $NAME set to "HE2" (string) CNSsolve> CNSsolve> set remarks=reset end CNSsolve> set remarks=accumulate end CNSsolve> CNSsolve> buffer message BUFFER> to=remarks BUFFER> dump BUFFER> end CNSsolve> CNSsolve> write structure output=&structure_outfile end ASSFIL: file hr64_h2o.mtf opened. CNSsolve> CNSsolve> write coordinates format=PDBO output=&coordinate_outfile selection=( known ) end SELRPN: 1189 atoms have been selected out of 1189 ASSFIL: file hr64_h2o.pdb opened. CNSsolve> CNSsolve> stop ============================================================ Maximum dynamic memory allocation: 8510272 bytes Maximum dynamic memory overhead: 800 bytes Program started at: 16:49:21 on 28-Feb-2011 Program stopped at: 16:49:23 on 28-Feb-2011 CPU time used: 0.4469 seconds ============================================================