[gmx-users] Force field for phosphoserine

[Justin Lemkul]

On 10/2/14 8:45 AM, ashish bihani wrote:
> Hello everyone,Has anyone subjected a polypeptide containing a phosphoserine residue to :~$ pdb pdb2gmx ? The program does not recognize serine as it has a phosphorus atom attached to it which is not present in the definition. I am trying to define phosphoserine as a residue (let's say PSER). Can anyone tell me what all files do I need to edit (what kind of data do I need to look for, to be more specific) in order to make the program recognize this new residue ?Thanks in advance for help.Regards,Ashish Bihani 		 	   		
>

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

Otherwise, find a force field that contains parameters already (most force 
fields use "SEP" as phosphoserine, not PSER).

-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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