[AMBER] MMPBSA Entropies: N-mode and Quasi Harmonic calculations

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 17 Jul 2012 13:38:16 +0200

I would be grateful if anyone could provide an explanation regarding the huge differences in total Delta S given by the two methods.

Below are the results obtained for exactly the same trajectories

Solvated complex topology file: 2wc6_bom_solv.prmtop
|Complex topology file: 2wc6_bom.prmtop
|Receptor topology file: 2wc6.prmtop
|Ligand topology file: bom.prmtop
|Initial mdcrd(s): prod_10ns.mdcrd
| prod_2ns.mdcrd
| prod_4ns.mdcrd
| prod_6ns.mdcrd
| prod_8ns.mdcrd
|
|Best guess for receptor mask: ":1-141"
|Best guess for ligand mask: ":142"
|Ligand residue name is "BOM"
|
|Calculations performed using 1000 frames.
|NMODE calculations performed using 20 frames.

DELTA S total= -21.7086 +/- 1.5570

ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:

DELTA S: -12.5924 -10.2513 -56.3566 -79.2006


Many thanks in advance

George


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Received on Tue Jul 17 2012 - 05:00:03 PDT
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