On Fri, 13 Mar 2015 11:32:09 -0400
David A Case <case.biomaps.rutgers.edu> wrote:
>
>
> > On Mar 13, 2015, at 11:20 AM, Hannes Loeffler
> > <Hannes.Loeffler.stfc.ac.uk> wrote:
> >
> > in a sequence like this
> >
> > p = loadpdb foo.pdb
> > solvateBox p TIP3PBOX
> > saveAmberParm p solvated.parm7 solvated.rst7
> > savepdb p solvated.pdb
> >
> > why is the origin in solvated.pdb in the box center contrary to the
> > inpcrd file?
>
> Historical preference. Use
>
> Set default nocenter on
>
> to avoid the translation
Ok but this operates on the prmtop only not the PDB. This would then
interfere with how sander and pmemd handle PBCs.
What I hoped I could do is to reuse this PDB in a later leap session
but centering happens through "solvatebox" and not with "setbox".
Many thanks,
Hannes.
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Received on Fri Mar 13 2015 - 09:30:02 PDT
