[apbs-users] APBS output visualization as movie/trajectory

[Nadeem A. V. <Nad...@ut...>]

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