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":
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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Received on Fri Jan 28 2011 - 00:00:03 PST