[gmx-users] MD localized in the active site

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 17 21:17:32 CET 2010


You also have to spend a sufficient amount of thought on the question
whether an approach like that will give you what you're after. It's
not going to sample a relevant ensemble and you're disabling the long
range correlations that may be of influence on ligand binding.



On Wed, Mar 17, 2010 at 9:01 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
>> 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
> 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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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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