[gmx-users] TOP file conversion
jalemkul at vt.edu
Wed Jul 2 12:19:19 CEST 2014
On 7/2/14, 12:27 AM, Andy Chao wrote:
> Dear GROMACS Users:
> I would like to convert a GRO file to the TOP file. Is it a better way to
> pdb2gmx -f device.gro -p device.top
> or to use
> g_x2top -f device.gro -ff oplsaa -o device.top?
That depends. If the contents of "device.gro" consist of a linear polymer of
definable units in the .rtp file, pdb2gmx is the way to go. If it is non-linear
or you don't have suitable .rtp entries, g_x2top may be better. In theory, you
can accomplish an equivalent result with either, but without more detail of
what's going on, there's no real solid recommendation to make.
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
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