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
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Received on Wed Feb 01 2012 - 10:00:02 PST
