[gmx-users] TOP file conversion

[Justin Lemkul]

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
> use
> 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

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

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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