Re: [gmx-users] Visualize Protein ligand complex

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 wrote: > Hi Sainitin, > > You can extract only the protein and ligand, using a suitable index file, > or you can limit the number of fram

Re: [gmx-users] Visualize Protein ligand complex

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

Re: [gmx-users] Visualize Protein ligand complex

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 > 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 >

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

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

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

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