Re: [gmx-users] Visualize Protein ligand complex

2013-07-04 Thread Sainitin Donakonda
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

[gmx-users] Visualize Protein ligand complex

2013-06-27 Thread Sainitin Donakonda
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

Re: [gmx-users] Visualize Protein ligand complex

2013-06-27 Thread Thales Kronenberger
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

Re: [gmx-users] Visualize Protein ligand complex

2013-06-27 Thread Tsjerk Wassenaar
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

Re: [gmx-users] Visualize Protein ligand complex after simulation

2013-01-28 Thread Justin Lemkul
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

Re: [gmx-users] Visualize Protein ligand complex after simulation

2013-01-28 Thread Erik Marklund
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