Re: [AMBER] Checking Sander energy values

From: Jason Swails <>
Date: Wed, 31 Jul 2013 08:41:53 -0400

On Wed, Jul 31, 2013 at 3:15 AM, FyD <> wrote:

> Dear Amber Users,
> Is there any way/program for checking/decomposing the energy values
> generated by Sander?
> For instance I am interested in looking at energy values bond by bond,
> angle by angle and dihedral by dihedral.
> Is there any debugging mode in Sander, which would allow studying that?

I don't see anywhere in either sander or NAB that prints out individual
energy terms, so I doubt this is possible any more.

> Before the 'Anal' program could be used; but my understanding is that
> is that Anal is compatible with 'plep' and not with 'LEaP'.

plep and anal both were before my time. My understanding is that LEaP
wrote the same prmtops that link, edit, and parm did. Of course the format
was changed ~10 to 11 years ago to make it more extendable, but you can
still write old Amber <=6-style prmtops in leap using the command

set oldprmtopformat on

somewhere in your leap script. Perhaps you can then use that prmtop with
anal, if you still have a copy laying around somewhere?

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 31 2013 - 06:00:04 PDT
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