|
Script # Homology modelling by the MODELLER TOP routine 'model'. # Demonstrates how to refine only a part of the model. # INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'alignment.ali' # alignment filename SET KNOWNS = '5fd1' # codes of the templates SET SEQUENCE = '1fdx' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 3 # index of the last model SET NONBONDED_SEL_ATOMS = 2 # selected atoms do not feel the neighbourhood CALL ROUTINE = 'model' # do homology modelling SET MODEL_SEGMENT = '1:' '2:' SET CLUSTER_CUT = 1.5 SET CLUSTER_METHOD = 'RMSD' # 'RMSD' | 'MAXIMAL_DISTANCE' SET EXPAND_CONTROL = 9999 9999 STARTING_MODEL ENDING_MODEL 0 # READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE CALL ROUTINE = 'cluster' # SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT='1:' '2:', SELECTION_SEARCH='segment', ; PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ; SELECTION_FROM='all', SELECTION_STATUS='initialize' RETURN END_SUBROUTINE Log: TOP_________> 608 652 WRITE_MODEL FILE = 'cluster.ini' openf5__224_> Open 14 UNKNOWN SEQUENTIAL cluster.ini wrpdb2__568_> Residues, atoms, selected atoms: 2 17 17 TOP_________> 609 653 READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v0}/modlib\/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL8v0}/modlib/models.lib TOP_________> 610 654 READ_PARAMETERS FILE = '$(LIB)/par.lib' openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v0}/modlib\/par.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v0}/modlib\/par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 611 655 READ_RESTRAINTS FILE = CSRFILE openf5__224_> Open 11 OLD SEQUENTIAL 1fdx.rsr openf5__224_> Open 11 OLD SEQUENTIAL 1fdx.rsr rdcsr2__307_> Number of restraints read : 0 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 openf5__224_> Open 11 OLD SEQUENTIAL 1fdx.rsr openf5__224_> Open 11 OLD SEQUENTIAL 1fdx.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: 3767 3767 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 TOP_________> 612 656 GENERATE_TOPOLOGY SEQUENCE = 'cluster' getf_______W> RTF restraint not found in the atoms list: residue type, indices: 20 2 atom names : C +N atom indices : 16 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 20 2 atom names : C CA +N O atom indices : 16 7 0 17 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 2 17 17 0 0 11 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 2 17 17 22 24 11 patch_______> segment topology patched using RTF: 2 ; TYR ; CTER segments residues atoms bonds angles dihedrals impropers: 1 2 18 18 24 26 12 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 2 18 18 24 26 12 TOP_________> 613 657 PATCH_SS_TEMPLATES TOP_________> 614 658 CALL ROUTINE = 'special_patches' TOP_________> 615 558 RETURN TOP_________> 616 659 WRITE_MODEL FILE = 'cluster.tmp' openf5__224_> Open 14 UNKNOWN SEQUENTIAL cluster.tmp wrpdb2__568_> Residues, atoms, selected atoms: 2 18 18 TOP_________> 617 660 OPEN OBJECTS_FILE = 'align.tmp' openf5__224_> Open 30 UNKNOWN SEQUENTIAL align.tmp openf5__224_> Open 30 UNKNOWN SEQUENTIAL align.tmp TOP_________> 618 661 WRITE OBJECTS = ALIGN_CODES TOP_________> 619 662 CLOSE TOP_________> 620 663 CALL ROUTINE = 'select_atoms' TOP_________> 621 807 PICK_ATOMS SELECTION_SEGMENT ='1:' '2:', SELECTION_SEARCH; ='segment', PICK_ATOMS_SET =1, RES_TYPES ='all', ATOM_TY; PES ='all', SELECTION_FROM ='all', SELECTION_STATUS ='ini; tialize' Number of atoms to choose from, total : 18 18 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 2 1: 2: selatm__462_> Number of selected atoms : 18 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ALA --- 2 : TYR 2 TOP_________> 622 808 RETURN TOP_________> 623 664 PICK_RESTRAINTS ADD_RESTRAINTS = off nselat__596E> Atom index is out of range (iatm,natm): 18 17 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2910609 2842.392 2.776 Starting time : 2005/06/16 16:52:10.687 Closing time : 2005/06/16 16:52:16.281 Total CPU time [seconds] : 5.56 |