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
--------------------------------------