Hi Ray,
Thanks for your answer. The problem is not limited to MMPBSA.py but is
in the pbsa code.
I have sent a more detailed bug report and solution:
http://archive.ambermd.org/201906/0179.html
Best regards,
Thomas Gaillard
Le Tuesday 18 June 2019 à 07:20:12AM, Ray Luo a écrit :
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
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 Wed Jun 19 2019 - 08:00:05 PDT
