We would need some of the error messages produced while you were running
these scripts. If you included the ones from MMPBSA.py that would be the
most helpful.
All the best,
Jason
On Wed, Jan 26, 2011 at 6:36 AM, 肖正涛 <xzt41.126.com> wrote:
> Dear amber professors,
> I am doing the free energy calculation between the protein and Mg2+
> using MM-PBSA with Amber10(both mm_pbsa.pl and MMPBSA.py),
> but many trials failed, when i check the temporary files, the following
> results were found in the "snapshot_lig.all.out":
> MM
> GB
> PB
> MS
> 1
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -465.1086
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> corrected reaction field energy: -733.413162
> surface area = 83.647
> ECAVITY = 83.647
> EDISPER = 0.0000
>
>
>
>
> I am confused with this, then i calculated the MM-PBSA energy of protein
> and the Na+, the same results was produced. Little information about this
> can be found by google, so i hope you can help me and give me some advices.
> thank you and best wishes to you!!
>
>
> Xiao Zhengtao ,
>
> Department of bioinformatics in Northwest Sci-Tech
> University of Agriculture and Forestry
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jan 26 2011 - 06:30:12 PST
