From: Daniel Aiello <Daniel.Aiello.umassmed.edu>
Date: Fri, 1 Jul 2011 10:06:23 -0400

We are using amber10 to simulate protein receptor-ligand complexes. We would like to visualize the electrostatic potential of these complexes. APBS seems to be a good option for generating electrostatic maps to be used as input for any number of molecular visualization software, we will most likely use jmol. I have compiled APBS, iAPBS, and sander.APBS. I've tried to compute binding energies with mm_pbsa.pl and APBS as the alternative PB solver. It appears to be working but my statistics.out file is empty and running the calculation manually with mm_pbsa_statistics.pl does not work. After reading documentation, I'm still not sure what the output files are supposed to contain when using mm_pbsa.pl with APBS? I'm not even sure I need to run sander.APBS in order to generate electrostatic maps. Also, I'm unclear on the methods for generating electrostatic maps with APBS for our simulations? I'm thinking of computing an average structure with ptraj, preparing this structure with PDB2PQR for electrostatic
s calcs, and then using APBS to generate an electrostatic map of this structure. I guess I am confused about the workflow involved in generating electrostatic maps from MD simulations. Any insight would be appreciated? Thanks,

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Received on Fri Jul 01 2011 - 07:30:03 PDT
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