On Mon, 2014-04-21 at 18:32 +0400, James Starlight wrote:
> Jason,
>
>
> many thanks for suggestions. The problems was exactly in the root
> permissions. By the way from the amber manual I've noticed that in new
> realize 3 different way's of MMPBSA calculations are realized. In this
> regard I wounder to know 1) if the existing MMPBSA on-line tutorial is
> still valid
Yes, it's still valid.
> and 2) what exactly MMPBSA method could be better for my task
> (analysis of the namd produced dcd trajectories with the conversion of
> the psf topologies to amber format)?
I suggest using MMPBSA.py. It supports DCD trajectories (as well as
every other trajectory format cpptraj recognizes) directly and generally
receives more support on the mailing list.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 21 2014 - 08:00:04 PDT
