Hi Tsjerk,
Thanks for information i limited number of frames ..which worked perfectly
:)
Cheers,
Sainitin
On Thu, Jun 27, 2013 at 8:06 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Sainitin,
You can extract only the protein and ligand, using a suitable index file,
or you can limit the
Hi,
I simulated protein ligand complex for 20 ns now i want to visualize this
complex after simulation in pymol.To look ligand interactions with protein
binding site
I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge
with solvent molecules so pymol couldnot visualize
Don't you wanna try to use the VMD
use vmd xxx.gro yyy.trr and then you could highlight your ligand
2013/6/27 Sainitin Donakonda saigr...@gmail.com
Hi,
I simulated protein ligand complex for 20 ns now i want to visualize this
complex after simulation in pymol.To look ligand interactions
Hi Sainitin,
You can extract only the protein and ligand, using a suitable index file,
or you can limit the number of frames.
Cheers,
Tsjerk
On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger
kronenberg...@gmail.com wrote:
Don't you wanna try to use the VMD
use vmd xxx.gro yyy.trr and
On 1/28/13 9:30 AM, Sainitin Donakonda wrote:
Hello,
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
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
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