Re: [AMBER] box's information

From: Jason Swails <>
Date: Fri, 8 May 2015 07:34:20 -0400

On Fri, May 8, 2015 at 3:42 AM, Fatemeh Sadat Alavi <>

> that's right. I use the new prmtop for heat's step that modified with
> and lost some information!

​What is your solvent? Did you use the CHARMM force field with chamber?
How did you modify your prmtop with ParmEd?

​ParmEd will automatically remove box information when it does not think
periodic boundaries are necessary anymore. In particular, it checks to see
if any solvent molecules are left in the list of residues, and if not,
deletes the periodic boundary information (the common use-case here is to
prepare a previously-solvated prmtop for use with implicit solvent models
by deleting the water).

What this means is that you need to use the "defineSolvent" command in
ParmEd to tell ParmEd to recognize more residue names as solvent to avoid
this behavior.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri May 08 2015 - 05:00:03 PDT
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