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

Diogo Vila Viçosa diogo.vicosa at fc.ul.pt
Wed Feb 3 11:37:04 CET 2016

This can help you:


Nevertheless, you can simply type: editconf -f structure.gro -o

On Wed, Feb 3, 2016 at 10:34 AM 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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