Jason,
many thanks for suggestions! Exactly I've forgot to provide tleap with set
box command defining box vectors manually only in the bottom of the inpcrd
file which was created initially without any box vectors together with the
prmtop file.
James
2014-06-10 21:48 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Tue, 2014-06-10 at 13:03 -0400, Brian Radak wrote:
> > But doesn't sander/pmemd adjust ifbox on-the-fly based on the lattice
> > vectors in the restart file? I've seen this happen with triclinic boxes
> for
> > example. I suppose the important thing is that ifbox > 0, which usually
> > requires you to use solvateBox or solvateOct in tleap or else set box.
>
> IFBOX never changes. It's a prmtop pointer (and sander/pmemd never
> modifies the prmtop file).
>
> I change it sometimes in ParmEd when deleting a periodic box (such as by
> removing solvent and ions), but that's to make sure IFBOX is consistent
> with what is expected by sander/pmemd... (Same thing with cpptraj --
> "nobox" triggers a change in IFBOX when using "parmwrite")
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue Jun 10 2014 - 12:00:02 PDT
