From: Radak, Brian K (bradak_at_anl.gov)
Date: Fri Jun 23 2017 - 13:10:51 CDT
Hi Hyun,
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.
HTH,
Brian
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov
________________________________
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
To: namd-l_at_ks.uiuc.edu
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.
Thanks
Hyun
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