- modeller_usage - salilab.org

Inclusion of zinc atoms, Add_restraint problem?
by Cardenas, Alfredo 28 Jan '05

28 Jan '05

Hi, I have a problem creating a model for a small protein with two zinc atoms. I use the ADD_RESTRAINT commands to create distance restrictions between the zincs and the residues attached to them. Looking at the log file, it looks that the restrictions are read without problems but at the end some ini file is read and I get an Atom index is out of bounds message. I am attaching the top, alignment and log file. I would appreciate any help. Thanks Alfredo Cardenas Top file: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment1.txt' # alignment filename SET KNOWNS = '1PTQ' # codes of the templates SET SEQUENCE = 'pkci' # code of the target #SET TOPOLOGY_MODEL = 1 SET HETATM_IO = on SET TOPLIB = '$(LIB)/top.lib' SET PARLIB = '$(LIB)/par.lib' #SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling SUBROUTINE ROUTINE = 'special_restraints' ADD_RESTRAINT ATOM_IDS = 'SG:14' 'ZN:55', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:17' 'ZN:55', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:39' 'ZN:55', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:42' 'ZN:55', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:31' 'ZN:54', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:34' 'ZN:54', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:50' 'ZN:54', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:53' 'ZN:54', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 RETURN END_SUBROUTINE Align file: C; alignment of catalytic domain ok PKCiota and PKCtheta >P1;1PTQ structureX:1PTQ:::::::: HRFKVYNYMSPTFCDHCGSLLWGLVKQGLKCEDCGMNVHHKCREKVANLC---/--* >P1;pkci sequence:pkci:::::::: HTFQAKRFNRRAHCAICTDRIWGLGRQGYKCINCKLLVHKKCHKLVTIECGRH/zz* Log file: MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Win2000 build 2195 Service Pack 4, C000826, uni, x86 Family 15 Model 2 Stepping 7 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2005/01/28 14:19:34.867 getprog_531W> ROUTINE redefined: special_restraints TOP_________> 108 746 SET ALNFILE = 'alignment1.txt' TOP_________> 109 747 SET KNOWNS = '1PTQ' TOP_________> 110 748 SET SEQUENCE = 'pkci' TOP_________> 111 749 SET HETATM_IO = ON TOP_________> 112 750 SET TOPLIB = '$(LIB)/top.lib' TOP_________> 113 751 SET PARLIB = '$(LIB)/par.lib' TOP_________> 114 752 SET STARTING_MODEL = 1 TOP_________> 115 753 SET ENDING_MODEL = 1 TOP_________> 116 754 CALL ROUTINE = 'model' TOP_________> 117 419 CALL ROUTINE = 'getnames' TOP_________> 118 531 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 119 532 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 120 533 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 121 534 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 122 535 SET ROOT_NAME = SEQUENCE TOP_________> 123 536 RETURN TOP_________> 124 420 CALL ROUTINE = 'homcsr' TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm Dynamically allocated memory at amaxbnd [B,kB,MB]: 1516107 1480.573 1.446 openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm read_al_374_> Non-standard residue type,position,sequence: z 54 2 read_al_374_> Non-standard residue type,position,sequence: z 55 2 Read the alignment from file : alignment1.txt Total number of alignment positions: 55 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 1PTQ 50 1 1PTQ 2 pkci 55 2 pkci TOP_________> 126 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 127 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./\1PTQ.atm check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND TOP_________> 128 118 CALL ROUTINE = GENERATE_METHOD TOP_________> 129 83 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm Read the alignment from file : alignment1.txt Total number of alignment positions: 50 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 1PTQ 50 1 1PTQ TOP_________> 130 84 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm Read the alignment from file : alignment1.txt Total number of alignment positions: 50 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 1PTQ 50 1 1PTQ TOP_________> 131 85 IF ARGUMENTS = INITIAL_MALIGN3D 0, OPERATION = 'EQ', THEN; = 'GO_TO NO_INITIAL_MALIGN3D' TOP_________> 132 88 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm read_al_374_> Non-standard residue type,position,sequence: z 54 2 read_al_374_> Non-standard residue type,position,sequence: z 55 2 Read the alignment from file : alignment1.txt Total number of alignment positions: 55 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 1PTQ 50 1 1PTQ 2 pkci 55 2 pkci TOP_________> 133 89 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib\/top.lib read_to_238_> Reading CHARMM residue topology file version: 22 1 openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL7v7}/modlib/models.lib TOP_________> 134 90 READ_PARAMETERS FILE = PARLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib\/par.lib Dynamically allocated memory at amattacns [B,kB,MB]: 1516657 1481.110 1.446 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib\/par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 135 91 CALL ROUTINE = 'create_topology' TOP_________> 136 106 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 53 atom names : C +N atom indices : 884 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 1 atom names : N -C CA H atom indices : 1 0 3 2 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 53 atom names : C CA +N O atom indices : 884 871 0 885 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 53 885 894 0 0 284 patch_______> segment topology patched using RTF: 1 ; HIS ; NTER segments residues atoms bonds angles dihedrals impropers: 1 53 887 896 1609 2350 284 patch_______> segment topology patched using RTF: 53 ; HIS ; CTER segments residues atoms bonds angles dihedrals impropers: 1 53 888 897 1611 2353 285 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 53 888 897 1611 2353 285 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 55 890 897 1611 2353 285 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 55 890 897 1611 2353 285 TOP_________> 137 107 CALL ROUTINE = 'default_patches' TOP_________> 138 526 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm read_al_374_> Non-standard residue type,position,sequence: z 54 2 read_al_374_> Non-standard residue type,position,sequence: z 55 2 Read the alignment from file : alignment1.txt Total number of alignment positions: 55 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 1PTQ 50 1 1PTQ 2 pkci 55 2 pkci TOP_________> 139 527 PATCH_SS_TEMPLATES TOP_________> 140 528 RETURN TOP_________> 141 108 CALL ROUTINE = 'special_patches' TOP_________> 142 523 RETURN TOP_________> 143 109 RETURN TOP_________> 144 92 TRANSFER_XYZ CLUSTER_CUT = -1.0 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 328 562 TOP_________> 145 93 BUILD_MODEL INITIALIZE_XYZ = OFF build___467W> All coordinates in MODEL have been assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates. TOP_________> 146 94 WRITE_MODEL FILE = MODEL openf5__224_> Open 14 UNKNOWN SEQUENTIAL pkci.ini wrpdb2__568_> Residues, atoms, selected atoms: 55 890 890 TOP_________> 147 95 RETURN TOP_________> 148 119 IF ARGUMENTS = EXIT_STAGE 2, OPERATION = 'EQ', THEN = 'RE; TURN' TOP_________> 149 120 IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'EQ', THE; N ='GO_TO __SKIP_RSRS' TOP_________> 150 121 CALL ROUTINE = 'mkhomcsr' TOP_________> 151 126 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS; = OFF Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: stereo r_stere_607W> Cannot find params in params file: CHARMM atoms : NY CA CPT H IUPAC atoms : NE1 CD1 CE2 HE1 Atom indices : 367 365 369 368 Residues : TRP TRP TRP TRP addprm__440W> Adding params (mean,force,period): 1.0268 60.0000 0 For atoms: NY CA CPT H r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 897 1611 1936 285 Total number of restraints before, now : 0 4729 make_re_422_> Number of previous, current restraints : 0 4729 make_re_423_> Number of previous, current selected restraints: 0 4729 TOP_________> 152 127 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm read_al_374_> Non-standard residue type,position,sequence: z 54 2 read_al_374_> Non-standard residue type,position,sequence: z 55 2 Read the alignment from file : alignment1.txt Total number of alignment positions: 55 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 1PTQ 50 1 1PTQ 2 pkci 55 2 pkci TOP_________> 153 128 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mnch1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PTQ getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4729 4780 make_re_423_> Number of previous, current selected restraints: 4729 4780 TOP_________> 154 129 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINT; S = 5 TOP_________> 155 130 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RE; STRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: omega_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/omega.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/omega.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PTQ getdata_289_> Proteins (all/accepted): 1 1 delete__442E> One or more atoms absent from MODEL: O: 53: C: 53: N: 54: CA: 54: delete__442E> One or more atoms absent from MODEL: O: 54: C: 54: N: 55: CA: 55: omgdel__425W> Unselected all O C +N +CA dihedrals: 52 make_re_422_> Number of previous, current restraints : 4780 4832 make_re_423_> Number of previous, current selected restraints: 4780 4780 TOP_________> 156 131 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: chi1_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PTQ getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4832 4878 make_re_423_> Number of previous, current selected restraints: 4780 4826 TOP_________> 157 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: chi2_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi2.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PTQ getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4878 4913 make_re_423_> Number of previous, current selected restraints: 4826 4861 TOP_________> 158 133 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: chi3_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi3.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PTQ getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4913 4928 make_re_423_> Number of previous, current selected restraints: 4861 4876 TOP_________> 159 134 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: chi4_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi4.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 1PTQ getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4928 4940 make_re_423_> Number of previous, current selected restraints: 4876 4888 TOP_________> 160 135 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINT; S = 5 TOP_________> 161 136 SET RES_TYPES = 'STD' TOP_________> 162 137 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE TOP_________> 163 138 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 164 139 SET RESTRAINT_GROUP = 9 TOP_________> 165 140 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 53 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 166 141 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 53 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 167 142 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 4940 5639 make_re_423_> Number of previous, current selected restraints: 4888 5587 TOP_________> 168 143 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DI; STANCE TOP_________> 169 144 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 170 145 SET RESTRAINT_GROUP = 10 TOP_________> 171 146 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : N Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 53 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 172 147 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : O Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 53 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 173 148 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 5639 6463 make_re_423_> Number of previous, current selected restraints: 5587 6411 TOP_________> 174 149 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_; DISTANCE TOP_________> 175 150 SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = OFF TOP_________> 176 151 SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5 TOP_________> 177 152 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 676 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 178 153 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : MNCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 212 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 179 154 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 6463 7008 make_re_423_> Number of previous, current selected restraints: 6411 6956 TOP_________> 180 155 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_; DISTANCE TOP_________> 181 156 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 182 157 SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0 TOP_________> 183 158 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 676 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 184 159 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 676 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 185 160 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 7008 7226 make_re_423_> Number of previous, current selected restraints: 6956 7174 TOP_________> 186 161 CALL ROUTINE = 'hetatm_restraints' TOP_________> 187 170 SET RESTRAINT_TYPE = 'distance' TOP_________> 188 171 SET DISTANCE_RSR_MODEL = 7 TOP_________> 189 172 SET MAXIMAL_DISTANCE = 7.0 TOP_________> 190 173 SET ADD_RESTRAINTS = ON TOP_________> 191 174 SET RESTRAINT_GROUP = 27 TOP_________> 192 175 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 193 176 SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 194 177 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : ALL Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 890 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 55 : ZN2 55 TOP_________> 195 178 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : HET Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 2 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 54 : ZN2 --- 55 : ZN2 2 TOP_________> 196 179 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 7226 7226 make_re_423_> Number of previous, current selected restraints: 7174 7174 TOP_________> 197 180 RETURN TOP_________> 198 162 CALL ROUTINE = 'blk_restraints' TOP_________> 199 183 SET RESTRAINT_TYPE = 'distance' TOP_________> 200 184 SET DISTANCE_RSR_MODEL = 7 TOP_________> 201 185 SET MAXIMAL_DISTANCE = 10.0 TOP_________> 202 186 SET ADD_RESTRAINTS = ON TOP_________> 203 187 SET RESTRAINT_GROUP = 27 TOP_________> 204 188 SET RESTRAINT_STDEV = 0.05 0.0 TOP_________> 205 189 SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = ON TOP_________> 206 190 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 207 191 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 208 192 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 7226 7226 make_re_423_> Number of previous, current selected restraints: 7174 7174 TOP_________> 209 193 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 210 194 SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 211 195 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : ALL Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 53 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 53 : HIS 53 TOP_________> 212 196 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'BLK' Number of atoms to choose from, total : 890 890 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 213 197 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 7226 7226 make_re_423_> Number of previous, current selected restraints: 7174 7174 TOP_________> 214 198 DELETE_ALIGNMENT TOP_________> 215 199 RETURN Dynamically allocated memory at amaxseq [B,kB,MB]: 5097041 4977.579 4.861 TOP_________> 216 163 CALL ROUTINE = 'special_restraints' TOP_________> 217 756 ADD_RESTRAINT ATOM_IDS = 'SG:14' 'ZN:55', RESTRAINT_PARAM; ETERS = 3 1 1 27 2 2 0 3.0 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 218 757 ADD_RESTRAINT ATOM_IDS = 'SG:17' 'ZN:55', RESTRAINT_PARAM; ETERS = 3 1 1 27 2 2 0 3.0 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 219 758 ADD_RESTRAINT ATOM_IDS = 'NE2:39' 'ZN:55', RESTRAINT_PARA; METERS = 3 1 1 27 2 2 0 3.0 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 220 759 ADD_RESTRAINT ATOM_IDS = 'SG:42' 'ZN:55', RESTRAINT_PARAM; ETERS = 3 1 1 27 2 2 0 3.0 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 221 760 ADD_RESTRAINT ATOM_IDS = 'SG:31' 'ZN:54', RESTRAINT_PARAM; ETERS = 3 1 1 27 2 2 0 3.0 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 222 761 ADD_RESTRAINT ATOM_IDS = 'SG:34' 'ZN:54', RESTRAINT_PARAM; ETERS = 3 1 1 27 2 2 0 3.0 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 223 762 ADD_RESTRAINT ATOM_IDS = 'SG:50' 'ZN:54', RESTRAINT_PARAM; ETERS = 3 1 1 27 2 2 0 3.0 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 224 763 ADD_RESTRAINT ATOM_IDS = 'NE2:53' 'ZN:54', RESTRAINT_PARA; METERS = 3 1 1 27 2 2 0 3.0 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 225 764 RETURN TOP_________> 226 164 CONDENSE_RESTRAINTS delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 7234 6845 TOP_________> 227 165 WRITE_RESTRAINTS FILE = CSRFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL pkci.rsr TOP_________> 228 166 SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = O; N top_mod_451W> Requested schedule step not available: 0 SCHEDULE_STEP set to N_SCHEDULE. TOP_________> 229 167 RETURN TOP_________> 230 122 LABEL __SKIP_RSRS TOP_________> 231 123 RETURN TOP_________> 232 421 IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'GE', THEN = 'RE; TURN' TOP_________> 233 422 CALL ROUTINE = 'rd_restraints' TOP_________> 234 276 READ_RESTRAINTS FILE = CSRFILE, ADD_RESTRAINTS = 'off' openf5__224_> Open 11 OLD SEQUENTIAL pkci.rsr openf5__224_> Open 11 OLD SEQUENTIAL pkci.rsr rdcsr2__307_> Number of restraints read : 0 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 openf5__224_> Open 11 OLD SEQUENTIAL pkci.rsr openf5__224_> Open 11 OLD SEQUENTIAL pkci.rsr rdcsr2__307_> Number of restraints read : 0 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 6845 6845 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 TOP_________> 235 277 RETURN TOP_________> 236 423 CALL ROUTINE = 'multiple_models' TOP_________> 237 202 DO ID2 = STARTING_MODEL ENDING_MODEL 1 TOP_________> 238 203 SET FINAL_MODEL = 'default' TOP_________> 239 204 CALL ROUTINE = 'single_model' TOP_________> 240 215 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 241 216 SET ID1 = 0 TOP_________> 242 217 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL pkci.D00000001 TOP_________> 243 218 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL pkci.ini openf5__224_> Open 11 OLD SEQUENTIAL pkci.ini rdatm___297_> Segments, residues, atoms: 2 55 438 rdatm___298_> Segment: 1 1 53 436 rdatm___298_> Segment: 2 54 55 2 TOP_________> 244 219 CALL ROUTINE = 'select_atoms' TOP_________> 245 288 PICK_ATOMS SELECTION_SEGMENT ='@:@' 'X:X', SELECTION_SEAR; CH ='segment', PICK_ATOMS_SET =1, RES_TYPES =; 'all', ATOM_TYPES ='all', SELECTION_FROM ='a; ll', SELECTION_STATUS ='initialize' Number of atoms to choose from, total : 438 438 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 55 1: 55: selatm__462_> Number of selected atoms : 438 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : HIS --- 55 : ZN2 55 TOP_________> 246 289 RETURN TOP_________> 247 220 CALL ROUTINE = RAND_METHOD TOP_________> 248 272 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 438 438 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 249 273 RETURN TOP_________> 250 221 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 251 222 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL pkci.sch TOP_________> 252 223 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 253 224 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 254 225 CALL ROUTINE = 'single_model_pass' TOP_________> 255 252 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 256 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 257 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF csrrng__299E> Atom index is out of bounds: 441 438 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 5094825 4975.415 4.859 Starting time : 2005/01/28 14:19:34.867 Closing time : 2005/01/28 14:19:42.305 Total CPU time [seconds] : 5.45 ************************************************************ Alfredo Cardenas Assistant Professor Department of Chemistry University of South Florida 4202 E. Fowler Ave, SCA 400 Tampa, FL 33620-5250 Phone: (813) 974-1591 Fax: (813) 974-1733 ************************************************************

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Re: [modeller_usage] problem
by vivek sharma 28 Jan '05

28 Jan '05

Dear Sir, I will try as per your directive. But, this problem is similar to one problem, which I found by searching 'NaN' in mailing list archives. http://salilab.org/archives/modeller_usage/2002/msg00189.html Actually , I am using one alignment and it finely generates 50 strs but in this particular case when I removed some terminal residues of target sequence, which I dont want to model, it gives this error. So there is a very minute change in alignment, and it produces this error and these removed residues are terminal residues of target sequence. Please have a look to weblink and suggest some more options if possible although I will try your advice. regards, Vivek Quoting Modeller Caretaker <modeller-care(a)salilab.org>: > vivek sharma wrote: > > I am a regular user of MODELER and I use 6v2. > > > > But now when I was generating 50 structures of a target using some > > templates, program ran fine till generating first 28 structures but > died > > in 29 structure generation with the error mentioned below (please see > > below). > > For, the first time I have observed this error. What can be the > problem. > > In the last statements of optimization schedule in log file you can see > > > the current value of energy is mentioned by 'NaN'. What does this mean, > > > looks like 'energy' has gone out of certain limits. > > NaN is 'not a number', and you're right - it probably means that the > energy has increased so much that it's gone out of the limits of the > datatype. You probably have a very bad initial structure, or an odd set > of restraints - you could try a short initial optimization to relax the > structure before trying to build your model. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > -- VIVEK SHARMA "You must be the change you wish to see in the world." MKG

1 0

problem
by vivek sharma 28 Jan '05

28 Jan '05

Dear Sir, I am a regular user of MODELER and I use 6v2. But now when I was generating 50 structures of a target using some templates, program ran fine till generating first 28 structures but died in 29 structure generation with the error mentioned below (please see below). For, the first time I have observed this error. What can be the problem. In the last statements of optimization schedule in log file you can see the current value of energy is mentioned by 'NaN'. What does this mean, looks like 'energy' has gone out of certain limits. 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 Initial value of energy before optimization : 35818.9410 Current energy : NaN Symmetry term within energy : 0.0000 Optimizer exit status : 1 Number of iterations : 1 Number of calls to energy function : 201 Number of updates of dynamic contacts : 1 Number of non-updates of dynamic contacts : 201 Final maximal atomic shift : 0.000 TOP_________> 7609 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 7610 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 7611 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 7612 238 END_DO TOP_________> 7613 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 7614 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 3854 49753 TOP_________> 7615 234 OPTIMIZE getcell_247E> Internal error: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 55660213 54355.680 53.082 Starting time : 2005/01/28 14:43:47.350 Closing time : 2005/01/28 18:09:34.578 Total CPU time [seconds] : 12315.51 Please have a look to the error, and suggest what can be the reason. I am first time facing such strange error, otherwise MODELER has worked fine always. Regards, Vivek -- VIVEK SHARMA "You must be the change you wish to see in the world." MKG

2 1

Other STACK PROBLEMS and Re: [modeller_usage] Modeller 7v7 Stack problems, tried EVERYTHING!!!!
by Carlos Luiz N. dos SANTOS 27 Jan '05

27 Jan '05

Dear all Modeller user, I follow by so near this question and answers because I have the same error message. I do the download of "Updated Windows binary" and I have the same problem of STACK OVERFLOW. I do my example (top scripts) exactly as the example from Modeller basic tutorial avec my data, of course. My sequence file is : >P1;rpb3 sequence:rpb3:::::::0.00: 0.00 MVALTVEELTPEHIRFTLSNTTVGYANALRRILISEVPTIAIDMVEIERNNTVLPDEVLA HRLGLIPIYSKRELKYKEECSCSGFCSECSVVFEIDVVHTDDTLRTVSTRDIVCDEEDVI IKSGPVITKLARDQGLKARCIGRKGVGKTHAKWSPVSAISFEYDKDNVRRETNYWFEESI EEEWPGVRQGEANLMQKIDKIHMCVEVVEGGAGPLAVVLEGLRILKEKVATLSSAAETMD * My script file is: # Example to ALIGN RPB3 with the Template # # the template is 1i50C (pdb1i50.ent at C:\Program Files\Modeller7v7\examples\Testes\atom_files) # SET OUTPUT_CONTROL = 1 1 1 1 0 # directory with input atom files SET ATOM_FILES_DIRECTORY = './:../atom_files' READ_MODEL FILE = 'pdb1i50.ent' SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1i50C', ATOM_FILES=ALIGN_CODES , ADD_SEQUENCE = on READ_ALIGNMENT FILE = 'rpb3.ali', ALIGN_CODES = ALIGN_CODES 'rpb3' ALIGN2D WRITE_ALIGNMENT FILE='rpb3-1i50.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='rpb3-1i50.pap', ALIGNMENT_FORMAT = 'PAP' I find an information at the FAQ messages that there are a Modeller's Variable called "MAXRES". I follow this suggestion from an modeller user: SET MAXRES=5000, and I did not get sucessful!!! but if I uses this ligne above: SET MAXRES = 50000000 I have no 'stack overflow' error message but I have '_E> modeller error message (se the log file above) Can you give some help ? Many thanks. My LOG file is : MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, WinXP build 2600 Service Pack 2, SANTOS, uni, x86 Family 15 Model 2 Stepping 9 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2005/01/24 12:06:44.218 TOP_________> 2 2 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 3 3 READ_MODEL FILE = 'pdb1i50.ent' openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\pdb1i50.ent openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\pdb1i50.ent rdatm___297_> Segments, residues, atoms: 10 3558 28279 rdatm___298_> Segment: 1 2 A 1450 A 11154 rdatm___298_> Segment: 2 18 B 1224 B 8711 rdatm___298_> Segment: 3 3 C 268 C 2095 rdatm___298_> Segment: 4 1 E 215 E 1760 rdatm___298_> Segment: 5 72 F 155 F 679 rdatm___298_> Segment: 6 2 H 146 H 1068 rdatm___298_> Segment: 7 1 I 122 I 997 rdatm___298_> Segment: 8 1 J 65 J 532 rdatm___298_> Segment: 9 1 K 114 K 919 rdatm___298_> Segment: 10 25 L 70 L 364 TOP_________> 4 4 SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1i50C', ATOM_F; ILES =ALIGN_CODES , ADD_SEQUENCE = ON TOP_________> 5 5 SET MAXRES = 50000000 TOP_________> 6 6 READ_ALIGNMENT FILE = 'rpb3.ali', ALIGN_CODES = ALIGN_COD; ES 'rpb3' openf5__224_> Open 20 OLD SEQUENTIAL rpb3.ali amaxres_215E> Dynamic memory allocation failed. Routine, variable, status: irestypn2 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2102291815 2053019.375 2004.902 Starting time : 2005/01/24 12:06:44.218 Closing time : 2005/01/24 12:08:38.125 Total CPU time [seconds] : 37.66 > Tom Petty wrote: > > I have a windows XP SP2 IBM laptop with plenty of memory (512MB > RAM) .... > >C:\Program Files\Modeller7v7\examples\tutorial-model>mod7v7 Toms-Initial >forrtl: severe (170): Program Exception - stack overflow > > > > This means that Modeller has exceeded the stack space limit. This a > constant, set when the Modeller binary was linked, so it won't help if > you add more memory to your machine. > ... > > Alternatively, you can download just such a 'fixed' binary from the > Modeller downloads page: > http://salilab.org/modeller/download_installation.html > (The link is right at the bottom: "Updated Windows binary".) > Use this binary to replace the existing mod7v7.exe file in your > Modeller installation (by default it should be in > C:\Program Files\modeller7v7\bin), and all should be well. > >If these problems persist, let me know. > > > Ben Webb, Modeller Caretaker > -- Dos Santos, Carlos Luiz N. Posdoctoral Cherc._/_/_/_/ _/_/_/_/ _/_/_/_/ _/ _/_/ _/_/_/_/ Campus de Cézeaux _/ _/ _/ _/_/ _/ _/ _/ _/ carlos(a)isima.fr _/ _/_/_/_/ _/ _/ _/_/_/ _/ _/ _/ T+33(0)473407662 _/ _/ _/ _/ _/ _/ _/_/_/_/ F+33(0)473405001 _/ _/ _/ _/ _/ _/ _/ UBP Aubière _/_/_/_/ _/_/_/_/ _/_/_/_/ _/ _/ _/ _/ http://www.isima.fr http://www.lamce.ufrj.br/carlos/francais

2 3

Disulfide bonds in dimer
by Vladimir Chupakhin 24 Jan '05

24 Jan '05

dear my modellers! I have a script question for you: I want tom model dimer from homopentamer, how is correctly define disulfide bonds *like this* CALL ROUTINE = 'model' # do homology modelling STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '166' '180' RETURN SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '160' '174' RETURN END_SUBROUTINE *or I need to define smthing like this* RESIDUE_IDS = 'A:166' 'A:180' RESIDUE_IDS = 'B:160' 'B:174' Yoz Vladimir Thanks in advance No virus found in this outgoing message. Checked by AVG Anti-Virus. Version: 7.0.300 / Virus Database: 265.6.11 - Release Date: 1/12/2005

2 1

(no subject)
by Johnwin Silvester 23 Jan '05

23 Jan '05

Cen Gao wrote: " Hi, I am new to modeller,Now I am just doing some simple test on a protein,but both the target and template has some atom file other than residue which i have to consider during the simulation.So i have to include the HETATM_IO = 'on' in simulation,my top file is as follow:" Hi, the problem may be here the template sequence count and the pdb sequence count is not same. In most pdb structures, we could find an amino acid missing at the begining. Verify whether the first template sequence aa is same with first aa in pdb sequence(spdbv control panel). probably you can get some other template of if theres no good alignment for that first amino acid, simply remove it. May this work regards, johnwin

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(no subject)
by Johnwin Silvester 23 Jan '05

23 Jan '05

Cen Gao wrote: " Hi, I am new to modeller,Now I am just doing some simple test on a protein,but both the target and template has some atom file other than residue which i have to consider during the simulation.So i have to include the HETATM_IO = 'on' in simulation,my top file is as follow:" Hi, the problem may be here the template sequence count and the pdb sequence count is not same. In most pdb structures, we could find an amino acid missing at the begining. Verify whether the first template sequence aa is same with first aa in pdb sequence(spdbv control panel). probably you can get some other template of if theres no good alignment for that first amino acid, simply remove it. May this work regards, johnwin

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doubt regarding modller usage
by E rajakumar 22 Jan '05

22 Jan '05

Sir I have installed modeller7v7 in windows2000. The input files are in 'C:/Program Files/Modeller7v7 after running the mod7v7 model-default, it could recognise model-default.top file but log file is showing that alignment file is not found please, could u mail me what is the problem? thank you in advance. rajkumar The log file is as follows MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Win2000 build 2195 Service Pack 2, E007A, uni, x86 Family 15 Model 2 Stepping 4 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2005/01/22 20:25:10.812 TOP_________> 109 749 SET ALNFILE = 'c:/Program Files/Modeller7v7/alignment' TOP_________> 110 750 SET KNOWNS = '1amu' TOP_________> 111 751 SET SEQUENCE = '1fax' TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = 'c:/Program Files/Modeller7v7/; 1amu' TOP_________> 113 753 SET STARTING_MODEL = 1 TOP_________> 114 754 SET ENDING_MODEL = 1 TOP_________> 115 755 CALL ROUTINE = 'model' TOP_________> 116 419 CALL ROUTINE = 'getnames' TOP_________> 117 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 118 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 119 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 120 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 121 538 SET ROOT_NAME = SEQUENCE TOP_________> 122 539 RETURN TOP_________> 123 420 CALL ROUTINE = 'homcsr' TOP_________> 124 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 fullfn__230E> File not found: c:/Program Files/Modeller7v7/alignment Directories: Extensions : :.ali Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 84067 82.097 0.080 Starting time : 2005/01/22 20:25:10.812 Closing time : 2005/01/22 20:25:12.140 Total CPU time [seconds] : 1.19 ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html

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Question on an error message
by Cen Gao 22 Jan '05

22 Jan '05

Hi, I am new to modeller,Now I am just doing some simple test on a protein,but both the target and template has some atom file other than residue which i have to consider during the simulation.So i have to include the HETATM_IO = 'on' in simulation,my top file is as follow: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'seq.ali' SET KNOWNS = '1U19' SET SEQUENCE = '1U20' SET TOPOLOGY_MODEL = 1, HETATM_IO = 'on', WATER_IO = 'on' SET TOPLIB = '$(LIB)/top.lib' SET PARLIB = '$(LIB)/par.lib' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' But it give me some error information rdabrk__290E> Number of residues in the alignment and pdb files are different: 696 697 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I don't why,because the alignment file and pdb file is exactly right(I simply generate the alignment file from the pdb file using modeller). And if I don't turn HETATM_IO = 'on' and simply using the code INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'seq.ali' SET KNOWNS = '1U19' SET SEQUENCE = '1U20' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' It works very well and give me the right target file.I am really confused about that.Can anyone give me some suggestion about my code.And I also wanna to ask if i want to take the non-residue atoms into consideration during modeller,is my method right?Thank you for your suggestion.

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Modeller multiple alignment
by Andreas Kowarsch 21 Jan '05

21 Jan '05

Hello all, i also tried to run my skript to create a multiple alignment. top-file: READ_MODEL FILE = '1HYZ.pdb', MODEL_SEGMENT 'FIRST:A''LAST:A' SEQUENCE_TO_ALI ALIGN_CODES = '1HYZ' READ_MODEL FILE = '1BIS.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = '1BIS',ADD_SEQUENCE = on READ_MODEL FILE = '1BIU.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = '1BIU',ADD_SEQUENCE = on SET ATOM_FILES = '1HYZ' '1BIS' '1BIU' MALIGN3D SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES READ_ALIGNMENT FILE = 'target.ali', ALIGN_CODES = ALIGN_CODES 'target', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='target.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='target.pap', ALIGNMENT_FORMAT = 'PAP' But my job don't terminate.... it always made the same log file log-file: Job starting time (YY/MM/DD HH:MM:SS): 2005/01/13 14:15:56.678 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2005/01/14 14:15:56.678 Closing time : 2005/01/14 14:15:57.612 Total CPU time [seconds] : 0.90 Please can anybody help me....

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