Dear Modeller users,
I'm getting a "dynamic memory allocation failed" message on a very small model. The test examples work fine, but when I modify model-full.py for my own use it gives a problem. Below I give the files I used, and the error message. I would appreciate any suggestions.
Ilya
model-full-test.py: ------------------------------------------------------------ # A sample script for fully automated comparative modeling
from modeller.automodel import * # Load the automodel class
log.verbose() env = environ()
# directories for input atom files env.io.atom_files_directory = './'
a = automodel(env, # file with template codes and target sequence alnfile = 'myalign.seg', # PDB codes of the templates knowns = ('1fjk', '1yod'), # code of the target sequence = '1qqq') a.auto_align() # get an automatic alignment a.make() # do homology modelling ------------------------------------------------------------ myalign.seg: >P1;1qqq sequence:1qqq:FIRST:@:52:@:phospholamban:Homo sapiens: 0:0 MDKVQYLTRSAIRRASTIEMPQQARQKLQNLYINRCLREICQELKEIRAMLK* >P1;1fjk structureN:1fjk:1:A:52:A:phospholamban:Homo sapiens:0:0 * >P1;1yod structureX:1yod:1:B:51:B:phospholamban:Homo sapiens: 1.80:0 ------------------------------------------------------------ 1fjk.pdb and 1yod.pdb files, downloaded from the PDB, are in the current dir.
model-full-test.log: -------------------------------------- Kind, OS, HostName, Kernel, Processor: 4, Linux optima 2.4.22-1.2199.nptl i686 Date and time of compilation : 06/20/2005 12:04:54 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2005/12/05 02:01:13.119
openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1fjk', '1yod'], atom_files=[], file='myalign.seg', (def)remove_gaps=True, (def)alignme\ nt_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True)
openf___224_> Open myalign.seg openf5__224_> Open 13 OLD SEQUENTIAL ./1fjk.atm
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124311 2074.522 2.026
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2125365 2075.552 2.027
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2299585 2245.688 2.193 openf5__224_> Open 13 OLD SEQUENTIAL ./1yod.atm
Read the alignment from file : myalign.seg Total number of alignment positions: 52
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1fjk 52 1 1fjk phospholamban 2 1yod 0 0 1yod phospholamban runcmd______> alignment.malign((def)rr_file='$(LIB)/as1.sim.mat', (def)off_diagonal=100, (def)local_alignment=False, (def)matrix_of\ fset=0.0, (def)overhang=0, (def)align_block=0, gap_penalties_1d=(-600, -400))
openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 malign__215E> Dynamic memory allocation failed. Routine, variable, status: rrdst 3
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