Dear Users'
I am performing free energy calculation with MM-PBSA.py for a crystal
structure of a protein-ligand complex.I have used MM-PBSA module after
running 10 ns md simulation.
Since I don't need gb namelist, I have used this input file:
*Input file for running PB and GB in serial&general startframe=1,
endframe=25000, keep_files=2,/&pb istrng=0.100, /*
Although I have checked the structure of the complex after production and I
am sure about the binding of ligand to its proper site, ÄG value is
positive. Here is the end part of the FINAL_RESULT.dat file:
*Differences (Complex - Receptor - Ligand):Energy Component
Average Std. Dev. Std. Err. of
Mean-------------------------------------------------------------------------------*
*BOND 0.0000 0.0001
0.0000*
*ANGLE 0.0000 0.0000
0.0000*
*DIHED 0.1101 0.1072
0.0024*
*VDWAALS -51.3535 4.0635
0.0908*
*EEL 106.0784 20.1745
0.4510*
*1-4 VDW 0.0000 0.0001
0.0000*
*1-4 EEL -0.0000 0.0001
0.0000*
*EPB -77.7007 17.4595
0.3903*
*ENPOLAR -42.1622 2.6622
0.0595*
*EDISPER 69.0762 4.0390
0.0903*
*DELTA G gas 54.8350 20.3812
0.4556*
*DELTA G solv -50.7868 17.6481
0.3945*
*DELTA TOTAL 4.0482 6.0860
0.1361*
I don't know where to look for the origin of this problem.
Best Regards,
--
Zeinab Tavasoli
PhD Student of Biophysics,
Tarbiat Modares University,
Tehran, Iran.
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Received on Wed Jul 02 2014 - 03:30:02 PDT
