[gmx-users] Translating .frcmod and .prep to .itp

[Justin Lemkul]

On 7/2/15 7:16 AM, Timofey Tyugashev wrote:
> I have parameters for 8-oxoguanine in FRCMOD and PREP files. Adding information
> from .prep file to dna.rtp an creating a modified entry in dna.hdb is simple
> enough.
> However I'm stuck now translating bond and angle data from .frcmod to .itp file,
> as its notation system is very different and its GROMACS manual section (5.3.3)
> lacks any substantial description of its formatting.

AMBER format:

http://ambermd.org/formats.html#parm.dat

> Is there any scripts or howtos for this, or at least a more detailed
> description  for ffbonded.itp?

See the comments in the file itself and the GROMACS manual.  This is just a 
matter of unit conversion.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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