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

[francesco oteri]

Hi,
if you were able to obtain a simulation it means you had a valid .top file!
In any case, gromacs recognises disulfide basing on the distance beween the
SG atoms.
In addition, the two chains are supposed to be in the same molecule.
So, my advice is, remove all the TER from pdb (but the last one), leave the
chain id and use pdb2gmx
with the option -chainsep ter. The result is supposed to be a topology
where your chain are grouped in
a single molecule,making possible to create the bridge, and at the same
time you keep the chain name
for future analysis.

Francesco


2013/3/19 shahid nayeem <msnayeem at gmail.com>

> 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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-- 
Cordiali saluti, Dr.Oteri Francesco