Dear Amber colleagues,
I am doing all the MMPBSA tutorials, and I found consistently that while the GENERALISED BORN results are almost identical to the tutorial (using the tutorial .mdrcd and .prmtop files) the POISSON BOLTZMANN results are completely different. As I said I only did the MMPBSA.py calculation, using given files. For example using the following command for tutorial files A 3.2 (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm <
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm>) I got the following FINAL_RESULTS_MMPBSA.dat file, which as you see for the POISSON BOLTZMANN yields a much lower DELTA TOTAL -6.6887 compared to the tutorial DELTA G binding = -41.7256 !!
Why is that?????
As explained above the GENERALISED BORN results are much more similar, for my calculation is DELTA TOTAL -52.3853 and the tutorial is DELTA G binding = -52.2672. That is great.
I used the command and input files provided on the tutorial:
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
I want to test this method on several systems, so it’s important for me to understand the differences…. any hint will really help me. The same happens on 3.1 so I suspect there is something different or wrong with the calculation.
Thanks a lot in advance,
Fabian
____________________
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
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Received on Mon Oct 19 2015 - 07:30:02 PDT
