[gmx-users] CHARMM36 for GMX
nedomacho at gmail.com
Wed Aug 2 20:52:19 CEST 2017
Yeah, those are indeed there for the particular molecules, thanks. I
understand that this is the only way to go, it's just that my use of GMX is
somewhat different in that I rarely use molecules in the normal sense, and
OPLS-AA, being a LEGO for simple groups, has been very convenient with that
catalog you mentioned. Like, place a carboxyl termination somewhere, or
have a hole in a bulk sheet of graphene, etc.
In any case, thank you.
On Wed, Aug 2, 2017 at 12:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 8/2/17 2:38 PM, Alex wrote:
>> Huh. Most of my work has been with OPLS-AA, so I took that for granted.
>> Where would the actual charges be, then?
> In the .rtp file, where residues are defined. Charges are not (and should
> not) necessarily be linked to atom types; they are a function of
> parametrized groups or molecules.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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