Re: [Apbs-users] Protein-protein binding free energy for MD trajectories

[Nathan B. <sob...@ya...>]

We've done this for a variety of protein datasets.  I usually start by running
psize.py (or pdb2pqr.py) on all of the input files to determine the largest
grid size needed for the calculations.  I then use the same grid settings
(number of grid points, spacings, etc.) for all snapshots from the run.  This
is easiest if you generate snapshot-specific input files from a template (e.g.,
using sed or equivalent).  You could probably use the actin-dimer example as a
starting point...

Good luck,

Nathan

--- Jerry Parks <jm...@du...> wrote:

> I have just installed apbs and would like to compute binding free energies
> for a fairly large number of pdb files. I have run MD on several docked
> protein-protein complexes in explicit solvent with NAMD and Charmm
> parameters. I have removed the solvent molecules and now I'd like to
> generate some sort of energetic comparison among the different docked
> configurations. I have also already generated the necessary pqr files for
> both the complex and the individual proteins.
> 
> Does anyone have experience with this type of calculation? What values
> should I use for the various input parameters? Does it make sense
> to calculate several energies over the course of an MD trajectory and
> then average the results so that I can compare energies from several
> trajectories? Any help with setting up these jobs would be greatly
> appreciated. I should mention that I'm not yet very familiar with apbs.
> 
> Jerry Parks
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> 


--
Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Washington University in St. Louis
http://cholla.wustl.edu