On Wed, Jul 31, 2013 at 3:15 AM, FyD <fyd.q4md-forcefieldtools.org> 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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 31 2013 - 06:00:04 PDT
