Re: [AMBER] Generating periodic box parameters for a pdb file already solvated

From: Jason Swails <>
Date: Thu, 26 Sep 2013 06:45:33 -0400

On Thu, Sep 26, 2013 at 1:54 AM, Sajeewa Pemasinghe <>wrote:

> Hi all,
> I have a snapshot pdb file which is already solvated and density
> equilibrated. Unfortunately the correspinding prmtop and inpcrd files were
> lost accidentally. Is there a way to create a prmtop/inpcrd files with box
> information using the pdb file I have?

Look at the 'setBox' command in tleap. This will set up an orthorhombic
box, though, so if you used a truncated octahedron you may need to set up
your box by hand after creating your system (which also includes some small
prmtop modifications).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Sep 26 2013 - 04:00:03 PDT
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