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 M. Callenberg
Ph.D. Candidate, Computational Biology
Carnegie Mellon University-University of Pittsburgh

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

Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery
and much more. Keep your Java skills current with LearnJavaNow -
200+ hours of step-by-step video tutorials by Java experts.
SALE $49.99 this month only -- learn more at:
apbs-users mailing list