[gmx-developers] difference between Protein and protein-H

Ming Tang m21.tang at qut.edu.au
Fri Nov 13 05:28:34 CET 2015

Thanks, Justin. Quite clear.

-----Original Message-----
From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Friday, 13 November 2015 9:30 AM
To: gmx-developers at gromacs.org
Cc: Discussion list for GROMACS users
Subject: Re: [gmx-developers] difference between Protein and protein-H

This is a user question that belongs on gmx-users, not gmx-developers. I am CCing this message to gmx-users; please continue any discussion there.

On 11/12/15 4:55 PM, Ming Tang wrote:
> Dear list,
> I want to calculate the number of intra-protein and protein-solvent H-bonds.
> Could anybody tell me the difference between "protein-H" and "protein" options ?

"Protein" is all protein atoms.
"Protein-H" is all protein non-hydrogen atoms (this isn't what you want to use).



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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