[gmx-users] topology

[shahid nayeem]

I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
shahid

On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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