There is no need to dump out frames or do anything manually.  You can get per-frame contacts for any set of atoms using g_mindist -on on the full trajectory.

Hi,

   First you should get specific frame (3000 ps in this example) instead of the whole trajectory as a pdb file use additionally the -dump option, e.g.

trjconv -f traj.xtc -s file.tpr -o time_3000ps.pdb -dump 3000

After getting pdb file of specific time you can view using PyMol or Chimera to see protein-ligand contacts.

regards

Hi,

Yes the ans provided by Mr.Chandrabhan is appropriate you should first using that command extract the required frame and then you can visualize the results or interaction in protein-ligand complex in discovery studio, chimera or pymol,etc. 

Thank you for the reply.

As I understand it, I must analyze frame by frame.

However, I found in VMD-List a script to analyze the contacts at frame by frame throughout the trajectory.

Regards,

Flavio

Hi,

Again back to my previous answer, you have to dumpp your full trajectory file into short time frames, for example, 100ps, 200ps, 300ps.......etc and then look for the contacts between protein and ligand in every pdb. you can view contacts of ligand to protein. you just follow either vmd manual for vmd or pymol manual or pymol.

regards

chandrabhan

There is no need to dump out frames or do anything manually.  You can get per-frame contacts for any set of atoms using g_mindist -on on the full trajectory.

Best way is to use g_contacts from here:

http://www.sciencedirect.com/science/article/pii/S0010465513002464

It is probably better to use something that will read directly from the DCD instead of dumping all the trajectory (which will result in a lot of disk space). Last time I did that I used mdanalysis ( http://leandro.iqm.unicamp.br/mdanalysis/home.shtml ), which uses as input a DCD file and a selection in VMD style and outputs the distance for every frame, and then I wrote a simple script to calculate how often the atoms were below a given threshold.