What happens, I think, is that mm_pbsa.pl fixes the surface tension to 1,
and then multiplies by cavity_surften while it's parsing the data. Not
sure why this is happening now, though.
I'd echo Qin's advice to try MMPBSA.py, though :).
All the best,
Jason
On Thu, Feb 2, 2012 at 3:49 PM, Qin Cai <qcai.uci.edu> wrote:
> Hi Therese,
>
> I'm just aware that the fixed coefficients were done on purpose. MMPBSA.py
> is a better choice if you want more freedom.
>
> Best,
> Qin
> On Feb 1, 2012, at 9:49 AM, Ray Luo, Ph.D. wrote:
>
> > Therese,
> >
> > I'm forwarding this to Qin for a look ...
> >
> > All the best,
> > Ray
> >
> > ---------- Forwarded message ----------
> > From: Therese Malliavin <terez.pasteur.fr>
> > Date: Wed, Feb 1, 2012 at 12:48 AM
> > Subject: [AMBER] about using MMPBSA Tan and Luo method in AMBER 11:
> > discrepancy in ECAVITY values
> > To: amber.ambermd.org
> >
> >
> > Dear AMBER Netters,
> >
> > I have some problems in using the Tan and Luo method with the
> > mm_pbsa.pl script from the AMBER 11 package. Indeed, the results
> > obtained with AMBER 11 are quite different from the ones obtained
> > with AMBER 9, as shown by the results obtained on the same snapshot:
> >
> > AMBER9:
> > 1
> > BOND = 1230.9291 ANGLE = 3154.2737 DIHED = 4051.0296
> > VDWAALS = -3251.8837 EEL = -29793.4172 HBOND = 0.0000
> > 1-4 VDW = 1505.8384 1-4 EEL = 14953.4064 RESTRAINT = 0.0000
> > corrected reaction field energy: -9780.831722
> > ECAVITY = 890.3956 EDISPER = -997.9678
> >
> >
> > AMBER11:
> > 1
> > BOND = 1230.9314 ANGLE = 3154.2736 DIHED = 4051.0294
> > VDWAALS = -3251.8840 EEL = -29793.4156 HBOND = 0.0000
> > 1-4 VDW = 1505.8386 1-4 EEL = 14953.4044 RESTRAINT = 0.0000
> > corrected reaction field energy: -9734.978826
> > ECAVITY = 20458.5423 EDISPER = -997.6458
> >
> > As you can see, all energy terms are closely similar, except the
> > ECAVITY which is much more larger in AMBER11 than in AMBER9. This much
> > larger energy
> > term then produce nonpolar solvation term of order of value larger than
> the
> > solvation polar term, and I find this quite strange.
> >
> > In mm_pbsa.pl with AMBER 11, I have been using the input parameter INP
> > in place of NOPT (NOPT seems to be obsolete, as far as I
> > understood?). Using INP permittted to get non-zero values for ECAVITY
> energy.
> > Then, I used SURFTEN and OFFSET options in place of CAVITY_SURFTEN
> > and CAVITY_OFFSET options. But, using SURFTEN, OFFSET or
> > CAVITY_SURFTEN, CAVITY_OFFSET does not change the ECAVITY value.
> >
> > Also, concerning the Tan and Luo method, I have seen that a article
> > describing it is still quoted "in preparation" in the
> > documentation. But, I had the impression that the method was published
> in:
> > .Article{ tan07,
> > author = {Tan C and Tan YH and Luo R},
> > title = {Implicit nonpolar solvent models},
> > journal = {J Phys Chem B},
> > volume = {111},
> > pages = {12263-12274},
> > year = {2007},
> > }
> >
> > I would much appreciate to get some information about using the Tan et
> > Luo method in AMBER 11.
> >
> > Best regards,
> > Thérèse
> >
> > Thérèse Malliavin
> > Unité de Bioinformatique Structurale
> > Institut Pasteur and CNRS UMR 3528
> > Paris, France
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Feb 02 2012 - 16:00:03 PST
