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