Hi Therese,
I was just checking the problem you described using the mm_pbsa.pl script in
AMBER 11 by setting SURFTEN to 1 and 0.0072, respectively.
In agreement with your observation the calculated numbers in the PREFIX.{com,
rec, lig}.all.out files are the same. However, the SURFTEN correction term is
applied afterwards in the mm_pbsa.pl script resulting into different GBSUR
values in the PREFIX_statistics.out file (and accordingly in different GBTOT
values).
Kind regards,
Simone
>
>
> 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 Fri Feb 03 2012 - 09:30:02 PST
