On Mon, Sep 5, 2011 at 10:15 AM, Ignacio J. General <ijgeneral.gmail.com>wrote:
> Actually, I think that if you know and understand what you want, then it is
> possible to use that energy in a sensible way. I do this kind of
> calculations myself and find them really useful. What you can do is to
> extract several frames (50, 100, several hundreds, experiment a little to
> find the optimum number) from your trajectory using ptraj, and then, in a
> script, do the following:
>
> 1) use ambpdb to create a pdb for each frame
> 2) use leap to load the pdb, use the "remove" command to remove the solvent
> in that frame, and then save the parameter and coordinate files.
> 3) Do a 1 step minimization of each frame in sander, to get the energy of
> that frame, i.e., of the solvent.
> 4) Take an average of all the frames.
>
This is more or less what MMPBSA does. You can also use ptraj to strip any
solvent out that you want and then trajout a series of PDBs (avoiding the
ambpdb and remove steps completely).
However, MMPBSA.py automates all of these steps, but requires you to choose
an implicit solvent model (which is an extra term than you'd have in the
explicit solvent phase, but you could always subtract those out afterwards).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Sep 05 2011 - 16:00:07 PDT
