Hi All,
I have recently installed Amber11 and AmberTool1.5. Before performing any
calculations, I am trying to reproduce the tutorial results. I successfully
completed the following tutorials:
Section 3.1<
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm>Calculate
the binding free energy of a protein-protein complex
Section 3.3<
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section3.htm>Calculate
the binding free energy of Ras-Raf and use Alanine Scanning to
compare to the binding energy of a mutant Ras-Raf complex that has had a
residue mutated to alanine and analyze the results.
The results matches well with the reported values. Now I proceeded further
to decomposition tutorial. While performing pair-wise residue decomposition
analysis, I am getting following error on my screen:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/bioschool/AMBER-11/amber11/bin/ptraj
sander found! Using /home/bioschool/AMBER-11/amber11/bin/sander for GB
calculations
sander found! Using /home/bioschool/AMBER-11/amber11/bin/sander for PB
calculations
Preparing trajectories for simulation...
50 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
I am strictly following the tutorial and was able to mimic the reported
results for section 3.1 and 3.3. Please let me know why I am getting this
error and How can I get rid of it? (Please find the attached mdout files)
Thanks and Regards,
Hirdesh
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Received on Thu Feb 09 2012 - 21:00:03 PST
