[gmx-users] crosslinking polypeptide chains
mark.j.abraham at gmail.com
Tue Feb 16 17:42:28 CET 2016
What Justin said, plus IIRC you'll have two complete hydrogenated chains
before specbond acts, so the two modified .rtp entries will want to have
temporary hydrogen atoms that may as well neutralize their respective
parts. specbond then strips them away, and you arrange for the result to
have whatever total charge makes sense.
On Tue, Feb 16, 2016 at 5:25 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> > 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
> 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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