[gmx-users] protein ligand tutorial

Albert mailmd2011 at gmail.com
Tue Jan 21 09:21:32 CET 2014

Many thanks for such kind and clear explanations.

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.....

best wishes

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

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