[gmx-users] Using g_mindist for calculating hydrophobic interaction between protein and ligand

[Justin Lemkul]

On 2/2/15 9:52 PM, Agnivo Gosai wrote:
> Dear Users
>
> I wish to characterize the hydrophobic interactions between a protein and a
> ligand by using the g_mindist analysis tool.
> I searched the forum and found a post which tells that it is supposedly the
> best tool available in gromacs for doing the job.
> Now , while reading the post a doubt cropped up in my mind.
> Do I need to provide an index file containing only the hydrophobic residues
> of the protein and the ligand ?

Not just that, but just the hydrophobic atoms.  Generally contact analysis 
focuses on heavy atoms, because hydrogens often inflate the totals.

> Or, just a normal index file with all the protein residues and ligand
> residues in two separate groups will do the job?

No, this would give you the total number of atomic contacts between the protein 
and ligand, which is not what you're after.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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