[gmx-users] Regarding topology...

[Justin Lemkul]

On 1/16/17 2:44 AM, Dilip H N wrote:
> My questions are..
> 1] how to create a topology file for ammonia.??
> 2] how to create a force field for ammonia, what is the residue name for
> ammonia in .pdb file.??
> 3] Why ammonia.itp is not  there in gromacs..??
> 4] Which force field to choose for ammonia..??
>

The CHARMM General Force Field (CGenFF) supports ammonia.  Its residue name is 
AMM1 and it is in our CHARMM36 port for GROMACS.  Use pdb2gmx on a suitably 
named coordinate file and you've got your topology.

http://mackerell.umaryland.edu/charmm_ff.shtml#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 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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