Re: [AMBER] MMPBSA radiopt effect on EDISPER

From: Ray Luo <rluo.uci.edu>
Date: Tue, 18 Jun 2019 07:20:12 +0800

Thomas,

Sorry for the late reply. Somehow your emails are put into the SPAM
folder by gmail.

The answer to your question is that in the newer releases, the inp=2
option no longer considers radiopt, which is only related to inp=1.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Tue, Jun 11, 2019 at 9:50 PM Thomas Gaillard
<thomas.gaillard.polytechnique.edu> wrote:
>
> Le Monday 13 May 2019 à 06:40:57PM, Thomas Gaillard a écrit :
> > Dear AMBER developers,
> >
> > Comparing MMPBSA results with radiopt option set to 0 or 1, I obtain
> > different values for the dispersion term (and of course for the PB term,
> > but the same value for the cavity term). Is this expected?
> >
> > This was already mentioned
> > (http://archive.ambermd.org/201702/0421.html).
> >
> > I was thinking that radiopt=1 would only affect the PB radii, not the
> > radii used for the cavity and dispersion terms.
> >
> > Thanks for your time,
>
> Hi,
>
> I am adding an example to illustrate my question.
>
> This is the PB test of MMPBSA.py
> (AmberTools/test/mmpbsa_py/02_Poisson_Boltzmann) with radiopt set to 0
> or 1:
>
> MMPBSADI radiopt=0
> &general
>    startframe=1, endframe=2, interval=1,
>    keep_files=0, debug_printlevel=2
> /
> &pb
>    istrng=0.1, inp=2, radiopt=[01],
> /
>
> Only the receptor energies are reported.
>
> radiopt=0:
> EPB                      -3255.0199
> EDISPER                  -1134.8265
>
> radiopt=1:
> EPB                      -3188.8747
> EDISPER                  -1128.0331
>
> Other terms (VDWAALS, EEL, ENPOLAR) are identical.
>
> I recall my question: is it expected that the EDISPER term is affected
> by radiopt?
>
> I can make other tests if it can help.
>
> Thanks,
>
> --
> Thomas Gaillard
> Professeur assistant
> Laboratoire de Biochimie
> Ecole Polytechnique
> 91128 Palaiseau cedex
> tel: +33 1 69 33 48 62
> fax: +33 1 69 33 49 09
> thomas.gaillard.polytechnique.edu
> http://thomasgaillard.fr
>
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Received on Mon Jun 17 2019 - 16:30:02 PDT