From: Robert Konecny <>
Date: Thu, 7 Jul 2011 10:48:21 -0700

Hi Dan,

as far as generating APBS electrostatic maps from MD simulations: you could
do what you are proposing - getting the structures from MD using ptraj then
running pdb2pqr and APBS to get the potential maps. But since you already
have sander.APBS you could do all this directly from sander. sander.APBS
can write out the potential maps for the given structure in DX format for
you. You could even run an MD simulation and have sander.APBS write out
elstat potential maps every n-th step.

If you are interested in only getting elstat potential maps from your final
structures - please take a look at example 5.1.4 from the iAPBS user guide This shows
how to set up such a calculation.



On Fri, Jul 01, 2011 at 10:06:23AM -0400, Daniel Aiello wrote:
> Hello, 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 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 does not work. After reading
> documentation, I'm still not sure what the output files are supposed to
> contain when using 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, Dan
> _______________________________________________
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Received on Thu Jul 07 2011 - 11:00:04 PDT
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