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

[shahid nayeem]

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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