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
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 cartoo
Hi,
Your tpr file only has information on the starting configuration (because
it's a file that stores everything you need to start your simulation, not a
file that contains your output). Your end point .gro file can be converted
into a pdb through editconf as well.
However, a better approach woul
This can help you:
http://manual.gromacs.org/programs/gmx-editconf.html
Nevertheless, you can simply type: editconf -f structure.gro -o
structure.pdb
On Wed, Feb 3, 2016 at 10:34 AM anu chandra wrote:
> Hello all,
>
> I just finished a short simulation of a membrane protein system and trying
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 w
