[gmx-users] Visualize Protein ligand complex after simulation
erikm at xray.bmc.uu.se
Mon Jan 28 15:42:47 CET 2013
Short answer is to inspect your complex with VMD or Pymol (or some
other viewer). Pymol takes pdb input, so unless your structure is
contained in a pdb file you must convert it with e.g. trjconv first.
If you want a single frame you need to extract one form your
trajectory, or, if the final frame form your simulation suffices, then
use the -c output from mdrun. Most likely you will want to take care
of the periodic boundary conditions, so a round of trjconv is probably
Ask again or look at the gromacs mailing-list archive if there is
anything specific that puzzles you.
On Jan 28, 2013, at 3:30 PM, Sainitin Donakonda wrote:
> Recently i started working on molecular dynamics on my protein ligand
> complex using gromacs i successfully did simulation but i dont know
> how to
> visualize this protein-ligand complex this after MD simulation
> Can any body tell me how to do it?
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users