[gmx-users] Amber to Gromacs

[Justin Lemkul]

On 4/30/14, 8:25 AM, Nash, Anthony wrote:
> Hi All,
>
> I've been thrown upon a project which requires the use of the Amber FF. I have a crystal structure .pdb and I wish to make a topology file using the AMBER ff99SB forcefield. The gromacs website directs me to the ffamber ports program, which seems to require Gromacs versions 3.1.4, 3.2.1, ..... 4.0. I, however, have access to Gromacs 4.6.1. Must I install an old version of Gromacs? If I must, what kind of issues am I going to face when I take my 3.* generated Gromacs topology file and run it on version 4.6.1? Or is this very out of date and there is something new?
>

Most of the Amber force fields are supported natively now; there is no need to 
download the ffamber ports so that information is indeed outdated.  Amber99-SB 
and Amber99-SB-ILDN are both built into Gromacs.

-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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