[gmx-users] topology

[Justin Lemkul]

On 3/18/13 10:49 PM, shahid nayeem wrote:
> I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
> shahid
>

My apologies.  For some reason I always think there is a -cys option, when in 
fact it is -ss.  In any case, if you're trying to treat some strange form of 
cysteine, some force fields have special names for different forms (CYM for 
thiolate, etc) so naming and proper force field choice may be the only viable 
mechanism here.

-Justin

> 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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-- 
========================================

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

========================================