------ Forwarded Message From: quentin kaas kaas@ligm.igh.cnrs.fr Organization: CNRS - IGH Date: Fri, 14 Mar 2003 15:19:15 +0100 To: modeller-care@salilab.org Subject: Array too small. Increase MPAIRS
I get a problem when I used Modeller when I do simple optimizations : "Array too small. Increase MPAIRS" I have seen in the archives that it was a problem with older version and I get and install the last version but it still give the same answer... Am I doing something wrong or is it a source code problem ?
My top file is :
SET OUTPUT_CONTROL = 1 1 1 1 1
READ_TOPOLOGY FILE = '$(LIB)/top_allh.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '../../1hsa' READ_ALIGNMENT FILE = 'model_MHCp.ali', ALIGN_CODES = '1hsa' 'MHCp' GENERATE_TOPOLOGY SEQUENCE = 'MHCp' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'MHCp.ini'
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = 'MHCp.rsr' SWITCH_TRACE TRACE_OUTPUT = 1, FILE = 'MHCp.trc' OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20
WRITE_MODEL FILE = 'MHCp.B'
Thanks in advance
Quentin Kaas, IMGT
------ End of Forwarded Message
Without seeing the input/output files, it probably indicates a difficult optimization problem that runs into many overlapping atom pairs. Can you improve the alignment?
Andrej
-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org
> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Modeller Care > Sent: Friday, March 14, 2003 6:32 PM > To: modeller_usage@salilab.org > Subject: FW: Array too small. Increase MPAIRS > > > > ------ Forwarded Message > From: quentin kaas kaas@ligm.igh.cnrs.fr > Organization: CNRS - IGH > Date: Fri, 14 Mar 2003 15:19:15 +0100 > To: modeller-care@salilab.org > Subject: Array too small. Increase MPAIRS > > I get a problem when I used Modeller when I do simple > optimizations : "Array too small. Increase MPAIRS" I have > seen in the archives that it was a problem with older version > and I get > and install the last version but it still give the same > answer... Am I doing something wrong or is it a source code problem ? > > My top file is : > > SET OUTPUT_CONTROL = 1 1 1 1 1 > > READ_TOPOLOGY FILE = '$(LIB)/top_allh.lib' > READ_PARAMETERS FILE = '$(LIB)/par.lib' > READ_MODEL FILE = '../../1hsa' > READ_ALIGNMENT FILE = 'model_MHCp.ali', ALIGN_CODES = '1hsa' 'MHCp' > GENERATE_TOPOLOGY SEQUENCE = 'MHCp' > TRANSFER_XYZ > BUILD_MODEL INITIALIZE_XYZ = off > WRITE_MODEL FILE = 'MHCp.ini' > > MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' > WRITE_RESTRAINTS FILE = 'MHCp.rsr' > SWITCH_TRACE TRACE_OUTPUT = 1, FILE = 'MHCp.trc' > OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 > > WRITE_MODEL FILE = 'MHCp.B' > > > Thanks in advance > > Quentin Kaas, > IMGT > > > ------ End of Forwarded Message >
I resolved my MPAIRS problem in using the top_heav.lib topology library instead of the top_allh.lib. As my model is quite big, the hydrogens may be too numerous to be handled by Modeller. Thank you for your help.
Quentin Kaas
Le Lundi 17 Mars 2003 16:08, Andrej Sali a écrit : > Without seeing the input/output files, it probably indicates a difficult > optimization problem that runs into many overlapping atom pairs. Can you > improve the alignment? > > Andrej
Possibly so.
Andrej
-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org
> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of quentin kaas > Sent: Tuesday, March 18, 2003 7:00 AM > To: modeller_usage@salilab.org > Subject: Re: Array too small. Increase MPAIRS > > > I resolved my MPAIRS problem in using the top_heav.lib > topology library > instead of the top_allh.lib. As my model is quite big, the > hydrogens may be > too numerous to be handled by Modeller. > Thank you for your help. > > Quentin Kaas > > Le Lundi 17 Mars 2003 16:08, Andrej Sali a écrit : > > Without seeing the input/output files, it probably indicates a > > difficult optimization problem that runs into many overlapping atom > > pairs. Can you improve the alignment? > > > > Andrej > >
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Andrej Sali -
Modeller Care -
quentin kaas