[gmx-users] .rtp file - how to define improper dihedrals?

[Justin Lemkul]

On 7/15/14, 8:57 AM, Dawid das wrote:
> Dear Gromacs experts,
>
> Let's say I want to keep in plane such a structure:
>
>            B
>             |
>            A
>          /    \
>         C     D
>
> What is the proper order of atoms for CHARMM22 force field in
> aminoacids.rtp file under
> [ impropers ] section?
>
> Is it:
>
> A C D B  0.0 200.0
> ?
> Does the order or C B and D matter at all? Or the central A atom should be
> at the end?
>

The central atom is listed first.  The order of the remaining three atoms should 
be irrelevant.  You can easily verify with single-point energy calculations.

-Justin

-- 
==================================================

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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