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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