# Re: AMBER: PMF

From: David Smith <David.Smith.cup.uni-muenchen.de>
Date: 16 Jul 2003 11:37:56 +0200

Dear Xiaojian Tan,

I am not really an expert in this matter but I have come across the same
thing in my research. I was not really worried about it because of the
following paragraph in the manual:

The procedure used to perform a PMF makes it difficult to separate
contributions due to the constraints themselves from those due to
non-bonded/electrostatic interactions. For this reason, in these cases
CORC will reflect the sum total of all three types of contributions and
the individual non-bonded/electrostatic contributions will be reported
as 0's.

To find out exactly why it is difficult to separate them I guess you
would need to read the papers in detail or ask David Perlman.

Good luck.

On Tue, 2003-07-15 at 19:02, X. Tan wrote:
> Dear amber users,
>
> A week ago, I sent this email to the list, but there is no response. So I
> would like to send it again in case there are some people who did not see it.
>
> I have a question about PMF calculation. Basically, I have performed a PMF
> calculation on two torsion angles with Gibbs, and I'd like to want to
> know how large the energy penalty would be for this conformational change.
> We expected to see a large value, but the calculated free energy is pretty
> small. In my output file, we found there was something which looks really
> suspicious: All the energy terms are zero except CORC...
>
> ELEC = 0.000 NONB = 0.000 14NB = 0.000
> 14EL = 0.000 BADH = 0.000 CORC = 0.108
> EPOL = 0.000 E3bod= 0.000
>
> Constrained Internals at Last F.E. Update Lam L+d_L
> L-d_L
> H1 (3352)-C1 (3351)-O1 (3353)-C7 (3354) -27.3650 -26.4000
> -28.3300
> C1 (3351)-O1 (3353)-C7 (3354)-C8 (3355) -123.7200 -125.0000
> -122.4400
>
>
> Could anyone tell me what has gone wrong with my calculation? Why
> ELEC, NONB, 14NB... are all Zero? Thanks for your attention. Any
> suggestion would be greatly appreciated!
>

```--
---------------------------------------
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Germany
Tel.: +49 (0)89 2180 77740
Fax.: +49 (0)89 2180 77738
e-mail: David.Smith.cup.uni-muenchen.de
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Received on Wed Jul 16 2003 - 10:53:01 PDT
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