[gmx-users] topology

[Justin Lemkul]

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

-- 
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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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