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

[francesco oteri]

If it works then you are right :)


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

> I did it. Simply I changed the name of Cys which forms interchain
> dsiulfide bond to CYS2 in the separated pdb file and I used G43a1
> forcefeild to run pdb2gmx. This gives a topology with same number of
> atom which is present in .xtc file. CYS2 is present .rtp file of G43a1
> forcefeild probably to form interchain disulfide bond reading from
> specbond.dat. Am I right in generating such half disulfide bond
> topology.
> shahid
>
> On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri
> <francesco.oteri at gmail.com> wrote:
> > 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
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-- 
Cordiali saluti, Dr.Oteri Francesco