[gmx-users] How to visualizing gro file in pymol

[Francesco Carbone]

I use to have the same problem and in my case it was cause by the fact that
I was using a different tpr file (cleaned from water).
When I started using the "untouched" tpr file (the one used during the
simulation) everything went fine using trjconv and the -dump option.

Fra

On 3 February 2016 at 10:43, Catarina A. Carvalheda dos Santos <
c.a.c.dossantos at dundee.ac.uk> wrote:

> Hi Anu,
>
> You can always use ediconf to convert your .gro file into a .pdb file =)
>
> For multiple chain systems Pymol needs the chain information in the
> structure file. Because .gro files don't have the chain info, you'll always
> need a .pdb file.
> If this is your case, that's the reason why the cartoon representation
> isn't working.
>
> Hope this helps,
>
> Cheers,
>
> On 3 February 2016 at 10:33, anu chandra <anu80125 at gmail.com> wrote:
>
> > Hello all,
> >
> > I just finished a short simulation of a membrane protein system and
> trying
> > to visualize the final gro file generated from the simulation using
> Pymol.
> > Unfortunately, the Pymol failed to visualize the protein in cartoon
> > representation. Though VMD can do the job, I just wonder is there a way I
> > can visualize the gro file in Pymol. A quick surfing on web suggested to
> > use the editconf to convert the .tpr file to .pdb file for visualizing
> with
> > Pymol. Unfortunately, here the .tpr file have structural information from
> > the beginning of the simulation rather than at the end of the simulation.
> >
> >
> > Any suggestion would be very much appreciated.
> >
> >
> > Many thanks
> > Anu
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> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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