Todd Geders said: >Hello all, > >Here is a simple script that automates the electrostatic potential >surface generation using Gromacs, MEAD, and Pymol for visualization. >It's exclusively based off of the post by Esben Peter Friis: >It requires you to massage your pdb file a bit, but it gets the job >done. Please glance at the comments in the script to see what I mean.
Thanks Todd for the script. I installed Gromacs 3.2 beta, MEAD 2.2.3 on Mac OS 10.3. The only change is that the $PDB.mdp file has to contain: cpp = /usr/bin/cpp to specify the cpp location in OS X. Run the script, seems to work. Now the question is how do I go about validating the results? I tried to compare one image I get with the one published for 1ALK.pdb but there were some differences :-(. Would anyone in the list be willing to send me the files for one of their proteins, so I can re-run the calculations and compare what I get? Thanks Michele Fuortes -- -- Michele Fuortes, M.D., Ph.D. Assistant Professor Departments of Surgery and of Cell and Developmental Biology Cornell University - Weill Medical College E-mail: mfuor...@med.cornell.edu
