[AMBER] output of MMPBSA.py

From: Markus Kaukonen <markus.kaukonen.iki.fi>
Date: Thu, 25 Aug 2016 13:43:20 +0300

Dear All,
I try to calculate the solvation energy of ethanol in water using MMPBSA.py
to do the GBSA and PBSA calculation.

QUESTION1: How do I set the dielectic constant for GBSA, could not find
parameter for that in the gb section in the manual?

My command was
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
eth_solvated.prmtop -cp eth.prmtop -y prod1.mdcrd

In the output file (FINAL_RESULTS_MMPBSA.dat) one has
for the generalised born:

GENERALIZED BORN:

Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 2.6689 1.5477
0.0979
ANGLE 3.5010 1.4781
0.0935
DIHED 1.4535 0.4764
0.0301
EEL 8.8759 1.0681
0.0676
1-4 VDW 0.2890 0.2154
0.0136
1-4 EEL -36.7120 1.1293
0.0714
EGB -9.9038 0.6543
0.0414
ESURF 1.3883 0.0028
0.0002

G gas -19.9237 2.1129
0.1336
G solv -8.5156 0.6537
0.0413

TOTAL -28.4393 2.0001
0.1265

-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using Quasi-harmonic Entropy Approximation: FREE ENERGY (G) = -50.7898
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------

QUESTION2: Which value is the solvation energy?

The input file:
Input file for running PB and GB
&general
endframe=999999, verbose=1,
entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/

Terveisin, Markus

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Received on Thu Aug 25 2016 - 04:00:03 PDT
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