[gmx-users] .top file from .tpr and .xtc

[shahid nayeem]

Hi
To be more clear I have .xtc file for a disulfide linked complex of
two chains. From this trajectory I can extract .xtc file for
individual chains. But when I generate .top file from individual chain
pdb I get one atom extra in .top file i.e. protonated SG of Cys which
I dont need in order to make my .xtc and .top file compatible.
Shahid

On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 3/18/13 12:35 PM, shahid nayeem wrote:
>>
>> Hi
>> Is it possible to write .top file from .xtc and .tpr using index.ndx
>> so that .top is available for tailormade components of simulated
>> protein.
>>
>
> All topology information is in the .tpr, but not in .top format.  You may be
> able to post-process the output of gmxdump to produce some hacked version,
> but that's just a bit of a hand-waving guess.  I don't really understand
> what your objective is.
>
> -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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