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AMBER Archive (2004)Subject: Re: AMBER: VS: mmpbsa question
From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Hi,
I think that from the information you provide below it is almost
Best regards
Holger
-----Opprinnelig melding-----
Hi Amber guys,
I ran an MMPBSA calculation on a set of 500 structures from
I got the following result : this is the delta column
complex1
Î?elec -743.63 (5.3 ) -523.56 (3.1)
Î?vdw -12.87 (2.0) -19.40 (2.0)
Î?int 11.59 (3.4) 40.93
Î?MM -744.91 ( 0.1) -502.03 (3.7)
Î?SA -4.07 (0.0) -2.54 (0.0)
Î?PB 929.22 (4.6) 593.17 (3.0)
Î?PBSA 925.15 (4.6) 590.62 (3.0)
Î?(PB +elec) 185.59 (2.8) 69.60 (2.7)
Î?(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
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
The vibrational part contribute most to it.
Thanks for your help in advance.
Layi
-- ++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Holger Gohlke
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