Dear Modellers,
What is the exact meaning of the columns in .rsr file? I think I have a
pretty good idea for all of them except two, but wouldn't mind if someone
can explain.
Happy modelling,
Mensur Dlakic
|>Hi,
|>
|>In principle, what you are trying to do is a fine idea and should be possible
|>to do something along those lines with MODELLER. Your problem may be a bug in
|>MODELLER or it may be a problem with the restraint file format as you use
|it, or
|>something else. There is no "1000" limitation on the number of
|restraints. Are
|>you specifying atoms by their integer indices or by their atom names (one has
|>to use the corresponding restraint file format)? Are you using hydrogens,
|>in which case the TOPOLOGY_MODEL has to be set to 1 and the GENERATE_TOPOLOGY
|>command has to be executed with the top.lib topology library, which contains
|>all hydrogens, not the default top_heav.lib? Are you defining pseudo atoms
|>and using restraints on pseudo atoms (indicated by the second error message),
|>the code for which is buggy?
|>
|>If this does not help, please email me the input files.
|>
|>Let's resolve this.
|>
|>Best, Andrej
|>
|>
|>> Dear Modellers,
|>>
|>> I am using experimental NOE restraints to improve models in case of weak
|>> homology between a target and its template. The NOE restraint file was
|>> included as:
|>>
|>> READ_RESTRAINTS FILE = 'nmr_2igh.rsr'
|>>
|>> However, when the file contains many entries (>1000 restraints), the
|>> following error message occurs:
|>>
|>> iup2crm_E> IUPAC atom not found in topology library: H
|>> act34___E> indpsd(i) out of range; ireal, natm: 0 2953
|>>
|>> The MODELLER runs fine when number of NOE entries is smaller than 500,
|>> and the output model shows improvement when using NOE restraints. I
|>> assume for restraint file with "MODELLER12 VERSION: USER FORMAT" has an
|>> upper bound for number of allowed entries. Is there any way that I can
|>> get around this problem?
|>>
|>> Thanks,
|>>
|>> -Dong Xu
|>> http://compbio.ornl.gov/~nxy
|>>
|>>
|>
|>
|>--
|>--
|>Andrej Sali, Assistant Professor
|>The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
|>tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
|>e-mail ; http://salilab.org
========================================================================
| Mensur Dlakic, PhD | Tel: (734) 764-3554 |
| Howard Hughes Med Inst | Fax: (734) 763-9323 |
| 4570 MSRB II | http://www-personal.umich.edu/~mensur/ |
| 1150 W Medical Center Dr | |
| Ann Arbor, MI 48109-0650 | E-mail: |
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