[gmx-users] phosphate amino acid

Justin Lemkul jalemkul at vt.edu
Wed Jan 22 20:18:52 CET 2014

On 1/22/14, 10:08 AM, Albert wrote:
> Hello:
> I am using charmm36 for MD simulations. There are some phosophate amino acids
> (including Ser and Thr) within my protein. I am just wondering is there any
> template in the 2014 update c36 FF? I opened the merge.rtp file and I am not
> sure whether they are there or not, since the name of each group is very
> difficult to recognize without a chemical scheme.

The residue names are identical to those in the CHARMM force field.  Those force 
field files are also free and available from the same webpage as the Gromacs 
files; they have full residue names and chemical structures.  Since it would 
have been a major pain to transfer the information over to Gromacs format in the 
conversion, we didn't.



Justin A. Lemkul, Ph.D.
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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