[gmx-users] Assigning charges to Proline residues

[Justin Lemkul]

On 8/30/16 11:28 AM, Dan Woodall wrote:
> Hello,
>
> I'm looking to define the charges on a 10 residue polypeptide using
> pdb2gmx. I want to have the N-terminus charged, and a proline at position 6
> charged, but I can only find ways to assign charges to the amino acids that
> typically carry charges. Is there a way I can force the program to
> recognize a +1 charge (protonated) on a proline?
>

You need to define a new residue entry in the .rtp file for this specific 
proline type, then assign that new residue name to the residue in the coordinate 
file.  See 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-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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