AQ2X - Converting distance restraints ------------------------------------- AQ2X - Aqua program directory: /u02/jurgen/src/aqua3.2 * * Processing coordinate file 1xxx_1.pdb into Aqua file * ===== Welcome to AquaWhat ===== version 3.2 called with arguments: set batch on exec aqua readone 1xxx_1.pdb write tmp quit Project name: 1xxx_1 (in StrucsetInit: Initialization of strucset <Set1> completed) Option <restrinp> (word): <none> Option <coordinp> (word): <none> Option <coordout> (word): <aqua> Option <element_guess_pdb> : <false> Option <terseness> (integer): <0> Main menu - choose command from: exec, set, read, readone, quit <Command read: set> <Command read: batch> <Command read: on> Option <batch> : <true> <Command read: exec> <Command read: aqua> <Command read: set> <Command read: coordinp> <Command read: pdb> Option <coordinp> (word): <pdb> Main menu - choose command from: exec, set, read, readone, quit <Command read: set> <Command read: oldmap> Ignoring option <oldmap> <Command read: off> Main menu - choose command from: exec, set, read, readone, quit <Command read: set> <Command read: restrinp> <Command read: diana> Option <restrinp> (word): <diana> Main menu - choose command from: exec, set, read, readone, quit <Command read: set> <Command read: multiple> Ignoring option <multiple> <Command read: off> Main menu - choose command from: exec, set, read, readone, quit <Command read: readone> (in ReadMenu: starting to read strucset <Set1>) (in ReadMenu: using the routines from AquaFuncts_io.c) <Command read: 1xxx_1.pdb> Will read 1042 atoms from each file Next file <1xxx_1.pdb>: (in Alloc_cv: memory allocated) Warning - rewinding the input file before reading next structure structure 1 read (in ToAqua_cv: allocating new molecule) (in FillAtoms_cv: allocating 1042 atoms in new molecule) (in MakeResidues: allocating 68 residues in molecule of strucset <Set1>) (in ToAqua_cv: allocating new structure) (in FillCoords_cv: allocating coordinates in new structure) Read 1 structure(s) from file <1xxx_1.pdb> (in Free_cv: memory freed) The set <Set1> now contains 1 structure(s) (in MapAtomsInSet: preparing to map atom names in strucset <Set1>) Now opening: /u02/jurgen/src/aqua3.2/data/AtomLIB-pdb (in ProcessAtomLIB: reading standard AtomLIB) (in ProcessAtomLIB: 982 atom name definitions read) (in MapAtomsInMol: mapping external to internal atom names) (in MapAtomsInMol: using routine FindAtom3) External atom name not found: (1) ASP 1 HT1 copying atom name instead External atom name not found: (1) ASP 1 HT2 copying atom name instead External atom name not found: (1) ASP 1 HT3 copying atom name instead External atom name not found: (67) VAL 67 OT1 copying atom name instead External atom name not found: (67) VAL 67 OT2 copying atom name instead External atom name not found: (68) ZIN 68 ZN1 copying atom name instead * One or more atoms could not be found in the AtomLIB <Command read: write> (in WriteMenu: starting to write strucset <Set1>) <Command read: tmp> Now opening: 1xxx_1_orig_tmp.set 1 structure has been written * Number of structures: 1 * Number of residues: 68 * Number of atoms: 1042 <Command read: quit> * * Processing restraint file 1xxx.noe * ===== Welcome to AquaHow ===== version 3.2 called with arguments: set batch on exec aqua mol orig tmp noe aqua 1xxx.noe out xplor 1xxx_noe.tbl ' Converted from 1xxx.noe (AQUA version 3.2)' quit Project name: 1xxx_1 (in StrucsetInit: Initialization of strucset <theSet> completed) Option <restrinp> (word): <none> Option <skip> : <true> Option <guess> : <true> Option <multiple> : <true> Option <sort> (word): <none> Option <terseness> (integer): <0> Main menu - choose command from: exec, set, sets, readinf, mol, quit <Command read: set> <Command read: batch> <Command read: on> Option <batch> : <true> <Command read: exec> <Command read: aqua> <Command read: set> <Command read: coordinp> Ignoring option <coordinp> <Command read: pdb> Main menu - choose command from: exec, set, sets, readinf, mol, quit <Command read: set> <Command read: oldmap> <Command read: off> Option <oldmap> : <false> Main menu - choose command from: exec, set, sets, readinf, mol, quit <Command read: set> <Command read: restrinp> <Command read: diana> Option <restrinp> (word): <diana> Main menu - choose command from: exec, set, sets, readinf, mol, quit <Command read: set> <Command read: multiple> <Command read: off> Option <multiple> : <false> Main menu - choose command from: exec, set, sets, readinf, mol, quit <Command read: mol> <Command read: orig> <Command read: tmp> Now opening: 1xxx_1_orig_tmp.set (in MakeResidues: allocating 68 residues in molecule of strucset <theSet>) A molecule has been read Coordinate set 1 has been read 1 Coordinate set has been read <Command read: noe> (in ProcessDRInput: Beginning restraint input) <Command read: aqua> <Command read: 1xxx.noe> Restraint-file <1xxx.noe> opened for reading in <Aqua simple restraint> format Will read 837 restraints (in ReadRestraintFile: expecting restraints of type NOE) * Read 837 distance restraints successfully! (in ProcessDRInput: Restraint input finished) (in MapDRInput: mapping atom names) (in MapAtomsInDRestraints: preparing to map atom names in the restraint list) Now opening: /u02/jurgen/src/aqua3.2/data/AtomLIB-diana (in ProcessAtomLIB: reading standard AtomLIB) (in ProcessAtomLIB: 489 atom name definitions read) (in MapAtomsIn1DR: mapping external to internal atom names) (in MapAtomsIn1DR: using routine FindAtom3) (in MapAtomsIn1DR: guessing ON) Option <restrinp> (word): <diana> External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HA copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 ZN copying atom name instead External atom name not found: (0) CYSZ 21 ZN copying atom name instead External atom name not found: (0) CYSZ 21 ZN copying atom name instead External atom name not found: (0) CYSZ 21 ZN copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 QB copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 HN copying atom name instead External atom name not found: (0) CYSZ 21 QB copying atom name instead External atom name not found: (0) CYSZ 21 QB copying atom name instead External atom name not found: (0) CYSZ 21 QB copying atom name instead External atom name not found: (0) CYSZ 21 QB copying atom name instead External atom name not found: (0) CYSZ 21 HB2 copying atom name instead External atom name not found: (0) CYSZ 21 HB3 copying atom name instead External atom name not found: (0) CYSZ 21 QB copying atom name instead * One or more atoms could not be found in the AtomLIB <Command read: out> (in ProcessDROutput: Beginning restraint output) <Command read: xplor> <Command read: 1xxx_noe.tbl> (in MapAtomsInDRestraints: preparing to map atom names in the restraint list) Now opening: /u02/jurgen/src/aqua3.2/data/AtomLIB-xplor (in ProcessAtomLIB: reading standard AtomLIB) (in ProcessAtomLIB: 677 atom name definitions read) (in MapAtomsIn1DR: mapping internal to external atom names) (in MapAtomsIn1DR: using routine FindAtom3) (in MapAtomsIn1DR: guessing OFF) Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HA copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 ZN copying atom name instead Internal atom name not found: (0) CYSZ 21 ZN copying atom name instead Internal atom name not found: (0) CYSZ 21 ZN copying atom name instead Internal atom name not found: (0) CYSZ 21 ZN copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 QB copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 HN copying atom name instead Internal atom name not found: (0) CYSZ 21 QB copying atom name instead Internal atom name not found: (0) CYSZ 21 QB copying atom name instead Internal atom name not found: (0) CYSZ 21 QB copying atom name instead Internal atom name not found: (0) CYSZ 21 QB copying atom name instead Internal atom name not found: (0) CYSZ 21 HB2 copying atom name instead Internal atom name not found: (0) CYSZ 21 HB3 copying atom name instead Internal atom name not found: (0) CYSZ 21 QB copying atom name instead * One or more atoms could not be found in the AtomLIB <Command read: '> <Command read: Converted> <Command read: from> <Command read: 1xxx.noe> <Command read: (AQUA> <Command read: version> <Command read: 3.2)'> * Distance restraints have been written (in ProcessDROutput: Restraint output finished) <Command read: quit>