[gmx-users] crosslinking polypeptide chains

Justin Lemkul jalemkul at vt.edu
Tue Feb 16 17:25:07 CET 2016

On 2/16/16 11:22 AM, Nash, Anthony wrote:
> Thank Justin and Mark,
> Apologies for not stripping out earlier content from my lazy “Reply”
> email. It was a slight of hand.
> It had crossed my mind to simply make two separate residues as you both
> suggested. Although I was trying to make most of this interchangeable with
> the Amber suite (this is an amber forcefield, but unlike my colleagues, I
> prefer working in Gromacs), in which XLeap can do this.
> However, with respects to Gromacs, what would happen to the charges? I
> would essentially have two charge groups if I split them, both not an
> integer, but when summed as a pair they would be 0 charge. Is this
> acceptable?

Nothing wrong with that at all.  AMBER doesn't use multi-atom charge groups,
anyway (and they're ignored by Verlet, too).



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


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