AMBER Archive (2002)

Subject: why are the results so large difference calculating by mm_pbsaandmm_gbsa?

From: Yongjun Jiang (yjjiang_at_mail.shcnc.ac.cn)
Date: Thu Sep 12 2002 - 02:25:32 CDT

Dear Dr.Holger Gohlke,

Yeah, I have gotten "corrected reaction field energy", after I revised the script of
mm_pbsa.pl to run well delphi. I have tested the examples in the tutorial with PB/GB,
all results are rights. Of course, I assigned my charge from amber parm94 and resp fitted,
but with the same radii as tutorial for delphi. The results of free energy from PB and
GB are very different.

I just saw the similar question from Mathy Froeyen here.
_____________________________________________________________________________

We did some mm_pbsa calculations.

The resulting final free energy differences
are positive ( using the Poisson Boltzman (PB) option).
 ******************
PBTOT 102.13 13.63
      ~~~~~~~
GBTOT -191.63 11.33
      ~~~~~~~~
********************
________________________________________________________________________________

What induces these results?

Thanks

Best regards.

Jiang
>
>
>
>
>>Hi,
>>
>>> Thank you very much your reply. yeah , I have revised it, and the delphi works well,
>>> not any questions. But the results are not rational.
>>
>>Do you get "corrected reaction field energy" lines in delphi that are <
>>0.0? And did you check that delphi properly assigns charges and radii? I
>>really can't believe that a solvation free energy is 0.0 - especially if
>>GB gives values below zero. If you like, you can send me one of your
>>delphi log files?
>>
>>Best regards
>>
>>Holger
>>
>>--
>>+++++++++++++++++++++++++++++++++++++++++++++
>>Dr. Holger Gohlke
>>Dept. of Molecular Biology, TPC15
>>The Scripps Research Institute
>>10550 N. Torrey Pines Rd.
>>La Jolla CA 92037 USA
>>phone: +1-858-784-9788
>>fax: +1-858-784-8896
>>email: gohlke_at_scripps.edu
>>+++++++++++++++++++++++++++++++++++++++++++++
>
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> Yongjun Jiang
> yjjiang_at_mail.shcnc.ac.cn
> 2002-09-12

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               Yongjun Jiang
               yjjiang_at_mail.shcnc.ac.cn
                                        2002-09-12