[AMBER] MMPBSA_Ras-Raf complex tutorial

From: Ruchika Bhat <ruchikabhat31.gmail.com>
Date: Wed, 5 Aug 2015 19:18:17 +0530

Hi Everyone,

I tried to replicate the ras-raf tutorial (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm) for
MMPBSA with the same files provided in the tutorial.
I was not able to replicate the same values in the Poisson Boltzman section
as the

ENPOLAR -50.9787 1.8037
0.2551
EDISPER 101.1385 2.6639
0.3767

DELTA G gas -1025.4769 34.3707
4.8607
DELTA G solv 997.2955 33.4313
4.7279

DELTA TOTAL -28.1814 8.1968
1.1592


values in my result file showed discrepancy with


ECAVITY -7.3062 0.3004 0.0425

DELTA G gas -1025.4769 1237.6138 175.0250
DELTA G solv 939.1189 34.5141 4.8810



DELTA G binding = -86.3579 +/- 8.3264 1.1775


values given in the tutorial file.

One observable change is the Ecavity in tutorial is replaced with ENPOLAR
and EDISPER values.


What is the causing this difference in values in PBSA values from -86 to
-28 kcal/mol. I used Amber14 for the run.


Regards,
Ruchika


My result .dat file is attached herewith.


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Received on Wed Aug 05 2015 - 07:00:02 PDT
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