It's really odd that CAVITY_SURFTEN and CAVITY_OFFSET doesn't change ECAVITY. After looking into the code, I found the CAVITY_SURFTEN and CAVITY_OFFSET are fixed to 1 and 0, respectively, in mm_pbsa.pl. So what you got for ECAVITY was actually the SAS area or the volume enclosed by SAS, depending on whether use_sav is 0 or 1. Please apply the attached patch in your $AMBERHOME so that your own CAVITY_SURFTEN and CAVITY_OFFSET will take effect.
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
>
>
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Received on Thu Feb 02 2012 - 13:00:02 PST
