[gmx-users] Intramolecular interactions

[Justin Lemkul]

On 6/22/14, 5:04 PM, Robson da Silva wrote:
> Dear gmx users, I have a question: how the program generates the
> intramolecular interactions? I mean, how the program recognizes the 1-2,
> 1-3 and 1-4 bonds between the atoms in the same molecule?
>
> I'm asking this because I'm developing a program and I can generate the
> intramolecular interactions if I specified the bonds in the .itp file but
> when I don't have bonds specified, I can't generate them. How the program
> does that?
>

Everything that pdb2gmx does in this regard is based on bonds.

-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 601
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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