Hi Nadeem,

I may be unaware of some functionality of one of the VMD plugins, but my guess is that you can only currently accomplish this by writing a TCL/Tk script (for VMD) or a pymol script. In these scripting languages you could loop over all of the frames of the trajectory and load each of the potential maps.

I have written a simple script for pymol that is posted on my website here: http://mem.bio.pitt.edu/content/animating-isosurfaces-pymol

It will require some modification for what you want to do however. In particular you will need to programmatically load the potential maps for coloring the surface (whereas I am simply loading the isocontour in the script above).

Keith


-- 
Keith M. Callenberg
Ph.D. Candidate, Computational Biology
Carnegie Mellon University-University of Pittsburgh
kmc112@{pitt,cmu}.edu
http://www.pitt.edu/~kmc112/


On Wed, Jan 16, 2013 at 12:29 PM, Nadeem Ahmad Vellore <Nadeem.Vellore@utah.edu> wrote:
Dear All,

I came across this thread<https://groups.google.com/forum/#!topic/apbs-users/lHRvQQaVSFI> regarding APBS calculation and VMD.

I have a simulation of a protein using AMBER and would like to visualize the trajectory using the electrostatic potential surface. After loading the prmtop/trj files, I calculated the electrostatics using the ABPS plugin in VMD and got the electrostatic map. I believe the calculated map loaded is for the currently displayed coordinates (frame 0). When I played the trajectory, I saw the map changing but that charge map loaded represent the initial coordinate potentials (please verify) and would mismatch during the rest of the trajectory.

I can surely extract few structures and calculate the electrostatic map, however, I want to see the electrostatic map for the trajectory to make a movie, rather than snapshots. Is that possible. I have installed the APBS software. If I write some representative PDB files (say 10 files) and run the electrostatic calculations and get 10 potential (dx) files, how will I load all of them to view as trajectory. Any hints would be highly appreciated.


Thanks and Regards
Nadeem


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