Developing a neutral arginine patch in a topology file

From: urmit shah (
Date: Fri Jun 19 2009 - 17:54:19 CDT

Dear all,
     I'm trying to generate a psf file for a non-solvated protein which
contains arginine as one of its residues. The isoelectric point of the
protein is around 11.00. The pdb file of the protein which I'm having is for
the protein at pH=7. So in order to make the protein neutral I want to
deprotonate some of the arginine(pH~10.7) residues on it. I'm using namd and
vmd for performing an MD. I'm unable to find a patch for the neutral
arginine residue. How can I generate the patch? Has anyone earlier done it?
Please guide.


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