On Wed, 2014-12-03 at 11:22 +0000, de Manzanos Guinot, Angela wrote:
> Hi again,
>
> Just to let you all know, that I solved the problem by commenting the
> line self.actions.append('autoimage') of the file make_trajs.py in the
> directory MMPBSA_mods. This seems to work fine, and now cpptraj
> generates the new trajectories without breaking down my protein.
I would recommend caution here. 'autoimage' typically does the "Right
Thing" with respect to imaging, although in some (rare) occasions, it
doesn't. In general, you need to image any explicit solvent
trajectories to make sure that you are simulating the receptor and
ligand in the *same* periodic cell (otherwise, binding energies come out
nonsensical).
So in the general case, imaging should be enabled. In the rare
instances when "autoimage" fails, my recommended approach is to prepare
the non-solvated trajectories yourself rather than request that
MMPBSA.py do it. What this means is use cpptraj to strip out all water
and ions, then simply do not provide a solvated prmtop ("-sp" flag) to
the MMPBSA.py command-line. In this case, the trajectory
imaging/stripping step will be skipped.
If nobody else is going to use your modified MMPBSA.py (or if they do,
they know that it is modified), then there is nothing wrong with your
approach. But it might bite you later on if you try using it and forget
you've disabled imaging.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 03 2014 - 04:30:02 PST
