[gmx-users] protein ligand tutorial

Justin Lemkul 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
> instance:
> 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
> Albert
> On 01/21/2014 07:15 AM, Tsjerk Wassenaar wrote:
>> Hi,
>> 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.
>> Cheers,
>> Tsjerk


Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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