Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory

From: Jason Swails <>
Date: Wed, 3 Sep 2014 06:43:57 -0400

On Wed, Sep 3, 2014 at 5:58 AM, wliu <> wrote:

> Hi,again
> I think I met another problem about my topology file. I have tried Dan's
> suggestion, and I use cpptraj to get the amber topology file named
> amber.prmtop:
> parm chamber22gro.prmtop
> parmwrite out amber.prmtop nochamber
> And I want to test if these two topology files give the same energy result

​No no. They won't. And they're not intended to. The amber.prmtop file
you generated is ONLY for analysis and visualization use. The only reason
this option exists is because some programs do not recognize chamber-style
topology files.

Again: _only_ use the chamber-generated prmtop to actually run simulations
and use the amber.prmtop file for programs that read standard Amber
topology files but not chamber-style topology files (like ptraj).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Sep 03 2014 - 04:00:02 PDT
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