On Mon, Jan 6, 2014 at 3:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Jan 6, 2014 at 1:28 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > I don't know what, if any, part of this is a bug. Presumably a stripped
> > trajectory should always have IFBOX = 0?
> >
>
> No, in many cases you may want to preserve unit cell information. This
> allows you e.g. to re-image in the future if you want (centering on a
> different part of the molecule) etc. Once you remove the box information
> you're stuck with the trajectory as-is.
>
This is a good point. As a whole, this idea is more applicable to cpptraj
than it is to ParmEd, since the latter is presumably used to prepare new
topologies for new simulations. The former, on the other hand, is likely
used as often to condense trajectories as it is to prepare topologies for
new simulations.
Perhaps the moral of the store is to use ante-MMPBSA.py (which uses ParmEd)
to create MMPBSA.py-compatible topologies. ;)
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 06 2014 - 18:00:02 PST
