Hello Dr. Schwieters,
Thanks a lot for your reply. I wanted to ask you for your suggestion in
the case of
structure calculation for protein along with the ligand. For a protein binding a
ligand, such
as ATP, is it recommended to do a full structure calculation along with
restraints for ATP?
Is the protocol for rigid body minimization followed by relaxation of the
binding residues
(e.g. prot_prot scripts) fine when compared to doing a full structure
calculation starting
from random coordinates?
regards
-kalyan
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> Hello kalyan--
>
>> I am trying to do a structure calculation of a dimeric protein along with
>> ligands.
>> I have got the ligand .pdb and .psf files from the hicup database. When I run
>> the program
>> I get back an error which is as follows
>>
>> -------------------------- Torsion Topology
>> ----------------------------------
>> WARNING: There are too many trees.
>> Please increase MAXTREE and re-run.
>>
>> %TORSION:TOPOLOGY-ERR: Fatal Topology Error
>
> this script uses the old torsion angle dynamics engine, which is
> deprecated. Please update your script to use the IVM (DYNAmics INTErnal
> in the XPLOR interface). Examples of its use can be found in
> e.g. eginput/protG/anneal.inp in the Xplor-NIH distribution.
>
> best regards--
> Charles
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Kalyan Sundar Chakrabarti
Lab # 207
Molecular Biophysics Unit
Indian Institute of Science
Bangalore 560012
Phone (080) 2293 2839 (Lab)
mobile: 0 9886842090
Alternative email: kalyansundarc at rediffmail.com
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