Re: [Apbs-users] Protein-protein binding free energy for MD trajectories
Biomolecular electrostatics software
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From: Nathan B. <sob...@ya...> - 2005-06-16 21:28:32
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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 > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu |