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

[francesco oteri]

Could you simply edit the file and removing the atom from [atoms] section ?
grompp wil complain regarding the line containing interactions. But also
these
few lines can be removed. Otherwise, vmd has the TopoTools that write the
.top
topology of the loaded pdb. Unfortunately, this topologyes are not useful
for carrying
out MD because they lack parameters. In any case are good for analysis!

Francesco


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

> Thanks Francesco.
> But my problem is exactly opposite. I do have a .top file containing
> both chain linked by disulfide bridge. I ran the simulation. Now I
> have extracted .xtc file for each chain separately and I want the
> corresponding, separate .top file for each chain. when I separate the
> pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is
> absent in .xtc file. So the .top file generated this way has one atom
> more as compared to .xtc file.
> shahid
>
> On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri
> <francesco.oteri at gmail.com> wrote:
> > 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
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-- 
Cordiali saluti, Dr.Oteri Francesco