-----Opprinnelig melding-----
Fra: Olayiwola Adekoya
Sendt: 28. april 2004 21:56
Til: amber.scripps.edu
Emne: mmpbsa question
Hi Amber guys,
I ran an MMPBSA calculation on a set of 500 structures from trajectories.
I got the following result : this is the delta column
complex1 complex2
Δelec -743.63 (5.3 ) -523.56 (3.1)
Δvdw -12.87 (2.0) -19.40 (2.0)
Δint 11.59 (3.4) 40.93 (3.4)
ΔMM -744.91 ( 0.1) -502.03 (3.7)
ΔSA -4.07 (0.0) -2.54 (0.0)
ΔPB 929.22 (4.6) 593.17 (3.0)
ΔPBSA 925.15 (4.6) 590.62 (3.0)
Δ(PB +elec) 185.59 (2.8) 69.60 (2.7)
Δ(MM +PBSA) 180.24 (3.3) 88.60 (3.3)
-TS -1088.37 (3.5) -1088.37 (3.5)
I was wondering why the difference in the electrostatic contribution from MM and that from Delphi. for the complex1,the electrostatic contribution from MM is -743.63 and 929.22 from delphi while for the complex2 -523.56 and 593.17 respectively. I was wondering why they were not consistent. I used the default values in the mm_pbsa.in script for the delphi calculations.
could anyone please explain why such difference?
the other question I have is about the value for -TS, -1088.37
the inhibitor is a protein with 102 residues, what could be sources of error.
The vibrational part contribute most to it.
Thanks for your help in advance.
Layi
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Received on Thu Apr 29 2004 - 23:53:00 PDT
