On 3/18/13 10:39 AM, shahid nayeem wrote:
Hi All
How can I get a topology file using pdb2gmx from a single chain
polypeptide with one of the CYS, SH in the form of SG as if it is
involved in disulfide linkage, while the other chain with which I
expect it to form disulfide link is not in the input pdb file. or can
I use pdb2gmx command and get the separate .top and .gro file for each
chain using index file.
You may be able to use the -cys option to fool pdb2gmx, but I don't know if that
will cause problems. Having half a disulfide present is odd, though some force
fields support thiolate or neutral (i.e. radical) forms of cysteine. You'll
have to look into the force field files to see what's available.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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