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

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Wed Feb 3 11:44:25 CET 2016

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,


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
University of Dundee
DD1 5EH, Dundee, Scotland, UK

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