[gmx-users] protein ligand tutorial
jalemkul at vt.edu
Tue Jan 21 15:55:56 CET 2014
On 1/21/14, 3:15 AM, Albert wrote:
> Many thanks for such kind and clear explanations.
Tjserk's explanation was quite right; I was over-thinking based on the fact that
there is one caveat to what he said. When running g_lie, the programs looks for
energy terms specifically labeled LIG-Protein, so you will have to create an
index group named "Protein" that encompasses whatever environment you want to
consider. The use of "Protein" in energygrps may cause problems elsewhere in
the .mdp file, so create index groups carefully.
> Can we extend this methods to evalute a peptide interact with the lipids? for
> energygrps = Protein POPC_solvent_ions
> I am not sure whether g_lie is suitable for membrane system or not.....
I'm not sure such a simple approximation would work. Generally, when people
study peptide-membrane binding, extensive PMF calculations are required. It
might be a good (albeit very computationally expensive) comparison to do.
> best wishes
> On 01/21/2014 07:15 AM, Tsjerk Wassenaar wrote:
>> Bound and "not hydrated" are completely different things. A ligand can be
>> partially exposed or may even be hydrated in a pocket. The difference
>> should be between ligand-environment1 interaction (solvent only) and
>> ligand-environment2 interaction (protein/solvent). So energygrps = Ligand
>> notLigand (or protein_solvent_ions) does make sense.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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