http://archive.ambermd.org/201101/0449.html
On Fri, Jan 28, 2011 at 2:47 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
>
>
>
>
> _______________________________________________
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> 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 Fri Jan 28 2011 - 06:00:05 PST
