Hi Amber users.
I've a crystallographic structure that involve an homodimeric enzyme, where
each monomer have two molecules of MgATP binding to it, one of this
correspond to the phosphoryl donor (MgATP catalytic) and the other one acts
as inhibithor of the enzymatic activity (MgATP allosteric). Also, each
monomer has an ion site near the two binding sites for MgATP. Kinetic
studies has revealed that pottasium bound to this site increases the
affinity for MgATP allosteric and the enzymatic inhibition. So, I'm
interested in calculate the binding energy for MgATP allosteric with and
without potassium bound to the ion site, using the method MM-PBSA, with one
minimized structure with explicit solvent, as described in this paper "J
Comput Chem 31: 797-810, 2010".
The prmtop file for the complex has the enzyme, with the four MgATP and the
two potassium ions.
The prmtop file of the receptor has the enzyme with the two MgATP catalytic
and thw two pottasium.
The prmtop file for the ligand has the two MgATP allosteric.
I only include the crystallographic waters in the files for the
minimization, also this file include the counter ions for neutralization.
I only use the last frame of the trajectory file (minimization.mdcrd) for
the calculations.
When I run MM-PBSA (MMPBSA.py) in amber11, the output file has no values of
binding free energy. This is the output file:
| Run on vie may 18 16:07:09 CLT 2012
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| keep_files=2, startframe=50,
|/
|&pb
| istrng=0.150,
|/
|&decomp
| idecomp=2, dec_verbose=3,
|/
|--------------------------------------------------------------
|Solvated complex topology file: ./toppar/complex_solvated-ions.prmtop
|Complex topology file: ./toppar/complex-nowt.prmtop
|Receptor topology file: ./toppar/receptor.prmtop
|Ligand topology file: ./toppar/ligando.prmtop
|Initial mdcrd(s): minimization.mdcrd
|
|Best guess for receptor mask: ":1-620:623-628"
|Best guess for ligand mask: ":621-622"
|Calculations performed using 2 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -4162.0960 0.0000
0.0000
EEL -34496.7736 0.0000
0.0000
EPB -14316.2634 0.0000
0.0000
ECAVITY 138.1355 0.0000
0.0000
G gas -38658.8696 0.0000
0.0000
G solv -14178.1279 0.0000
0.0000
TOTAL -52836.9975 0.0000
0.0000
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS nan nan
nan
EEL inf nan
nan
EPB -12535.4077 0.0000
0.0000
ECAVITY 136.7652 0.0000
0.0000
G gas nan nan
nan
G solv -12398.6425 0.0000
0.0000
TOTAL nan nan
nan
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -14.6917 0.0000
0.0000
EEL 2097.2930 0.0000
0.0000
EPB -1720.7177 0.0000
0.0000
ECAVITY 5.8754 0.0000
0.0000
G gas 2082.6013 0.0000
0.0000
G solv -1714.8423 0.0000
0.0000
TOTAL 367.7590 0.0000
0.0000
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS nan nan
nan
EEL -inf nan
nan
EPB -60.1380 0.0000
0.0000
ECAVITY -4.5051 0.0000
0.0000
DELTA G gas nan nan
nan
DELTA G solv -64.6431 0.0000
0.0000
DELTA G binding = nan +/- nan
nan
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Can anyone tell me what i'm doing wrong? or some suggestion?
Thanks in advance.
Alejandro Blanco
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Received on Tue May 22 2012 - 16:00:02 PDT
