Re: [AMBER] How do I use for namd .dcd file?

From: Jason Swails <>
Date: Mon, 23 Sep 2013 07:04:30 -0400

A couple more comments:

On Sun, Sep 22, 2013 at 7:13 PM, sudipta <> wrote:

> [snip]
> Do I need to use program for generating the .prmtop file
> for running program. If so how do I use that? Is there any
> significant difference between AMBERtools12 and AMBERtools13 for running
> program

No, is never necessary if you create all of the needed
topology files in the beginning, prior to running any calculations (as is
recommended practice). is particularly useful when you
decide to do MM/PBSA calculations on a system after creating the topology
file and you don't happen to have the files you need to create them through

However, does _not_ work with chamber-generated topology
files, so that's not even an option in your case. As for the 12 vs. 13
difference, AmberTools 13 has more bug fixes and more stable PBSA options
than AmberTools 12 in terms of the default solvation radii for the
non-polar solvation free energy part of the calculation.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 23 2013 - 04:30:02 PDT
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