Re: [AMBER] leap and centering

From: David A Case <>
Date: Sat, 14 Mar 2015 09:31:56 -0400

On Fri, Mar 13, 2015, Hannes Loeffler wrote:
> > >
> > > 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?

Sorry: I misread your original post. This is definitely undocumented, and
odd/buggy behavior. I'll file a bug report to try to get things sorted.
(But see below for my questions about what priority this should have.)

> > Set default nocenter on
> >
> Ok but this operates on the prmtop only not the PDB. This would then
> interfere with how sander and pmemd handle PBCs.

I don't see this. The prmtop file is unaffected (as I would expect) by the
presence or absence of this default setting. With nocenter set to "on",
solvated.pdb and solvated.rst7 have the same coordinates. And since the
different files seem to differ by just translations, PBC's in sander and pmemd
should be unaffected. What am I missing here?

...thanks for the report....dac

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Received on Sat Mar 14 2015 - 07:00:02 PDT
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