[AMBER] issues with MMPBSA tutorial/MMPBSA.py

From: Bennion, Brian <Bennion1.llnl.gov>
Date: Fri, 13 Dec 2013 19:03:42 +0000

I am trying to figure out some issues with the mmpbsa tutorial.

Following the MMPBSA tutorial with all the files that are provided on the website gives the expected results using our recently compiled amber12 code. With the exceptions noted below it is incredibly easy to follow and understand.

However, when starting with the ras-raf, ras, raf pdb files and following the tutorial exactly by creating my own prmtop and inpcrd files, a nasty python error is generated. Googling that error tells me that there is a problem with reading text and assigning it to variables but not in relation to anything AMBER. This error occurs at the Mutating trajectories step of the mmpbsa calculation.

comparing the prmtop files that I created to those provided on the website reveal several additional sections not present in the ~2006 files provided in the tgz archive on the website.
This error is shown below.
There are also some typos in the website that caught me off guard, namely the use of hyphens in names of some files in some places and the hyphen is gone in other places on the website.
Any assistance is appreciated.
Brian Bennion

bennion1 284:~/lscratchc/TBP/amberWork/tutorials$ MMPBSA.py -O -i mmpbsa.in -sp ras-raf_solvated.prmtop -cp rasraf.prmtop -rp ras.prmtop -lp raf.prmtop -y prod1.mdcrd -mc rasraf_mutant.prmtop -mr ras_mutant.prmtop
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /usr/gapps/cchem_software/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /usr/gapps/cchem_software/amber12/bin/cpptraj
Preparing trajectories for simulation...
Mutating trajectories...
TypeError: not all arguments converted during string formatting
Exiting. All files have been retained.

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Received on Fri Dec 13 2013 - 11:30:02 PST
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