Hi Ray,
I have done my tests with up-to-date (I think) AmberTools19 (revision
3). Have you tried my simple example on Na+ described in the following
message?
http://archive.ambermd.org/201906/0179.html
Thomas
Le Thursday 20 June 2019 à 05:14:11AM, Ray Luo a écrit :
> Hi Thomas,
>
> I've just checked the Amber 19 release ... looks like radiopt doesn't
> change energy values in inp=2 calculations.
>
> 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 Wed, Jun 19, 2019 at 10:51 PM Ray Luo <rluo.uci.edu> wrote:
> >
> > Thomas,
> >
> > Thanks a lot for reporting! Let me take a look ...
> >
> > 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 Wed, Jun 19, 2019 at 10:49 PM Thomas Gaillard
> > <thomas.gaillard.polytechnique.edu> wrote:
> > >
> > > 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
--
Thomas Gaillard
Professeur assistant
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
France
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 - 16:00:02 PDT
