Re: [AMBER] leap and centering

From: <>
Date: Sun, 15 Mar 2015 08:52:02 +0000

Yes, right, I should have said inpcrd instead of prmtop. The coordinates will be the same with "nocenter" but the origin will be in the center of the box. This means that sander/pmemd will "break" the simulation box into eight little ones. While this is fine as far as PBCs go it's obviously not particular convenient for visualisation (not to mention to explain this to users).

Many thanks,

From: David A Case []
Sent: 14 March 2015 13:31
To: AMBER Mailing List
Subject: Re: [AMBER] leap and centering

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 Sun Mar 15 2015 - 02:00:02 PDT
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