Anna Marabotti wrote:
Dear gmx-users,
I'd like to perform a molecular dynamics simulation on a protein-ligand
complex, in such a way that only residues belonging to the active
site can move, whereas the rest of the protein is kept fixed. I searched
for some information about how to do it with GROMACS, but I didn't find
anything.
Could anybody give me some suggestions about this subject, please?
You could create a custom posre.itp (using genrestr) to restrain whatever atoms
you choose, but it won't speed up your calculations in any way, if that's what
you're after. You could also specify freezegrps in the .mdp file, which
requires a custom index group; it may be more difficult to use this setup based
on the types of exclusions that would be necessary within whatever is frozen.
-Justin
Many thanks in advance and regards.
Anna
__________________________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: [email protected] <mailto:[email protected]>
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you're too small to make a change, try sleeping with a
mosquito"
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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