From: Radak, Brian K (bradak_at_anl.gov)
Date: Fri Jun 23 2017 - 13:10:51 CDT
Such a residue is not, to my knowledge, part of the CHARMM36 force field. I don't know if there is a recommended procedure or prescription for extending that force field directly, but there are a number of tools for small organic molecules that might be useful, specifically CGenFF, FFTK, and GAAMP.
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From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Hyun <biophysics1_at_gmail.com>
Sent: Friday, June 23, 2017 11:43:38 AM
Subject: namd-l: topology file for the residue CSO
Dear NAMD users
I am trying to find the CHARMM topology file for an oxidized cysteine. ( ex. the residue CSO in 1oet.pdb )
Is there any patch or the CHARMM topology file for an oxidized cysteine ?
Also, could you explain how to generate the topology file for an oxidized cysteine (Cys—SOH) if there is no available topology for it ?
Recommending tutorials or summary of method will be helpful.
I don't have an experience for building the topology file, but if I will try.
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