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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

|>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:                  |