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[modeller_usage] Pick Restraints



I'm still trying to get to the end of my clustering script.  Your last bit of advice got me further, but I've come up against another error that I can't solve, an "Atom index is out of range " error. At first I thought this occurred because the sequence was being patched with an OXT, but I get exactly the same error even if I prevent that. Below are my script and the last part of the log. Sorry to bother you so much!

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