Hello Mani,
Are you using amber12?
This error is not any happened to systems with metal ions, it also happend
to my calculations when I using amber12.
MM-GBSA works fine with MMPBSA.py script. However, MM-PBSA keep giving me
the same error as yours. Here is a sample out put file of my calculation:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /global/software/amber-12/bin/mmpbsa_py_energy
cpptraj found! Using /global/software/amber-12/bin/cpptraj
Preparing trajectories for simulation...
10 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with
/global/software/amber-12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with
/global/software/amber-12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /global/software/amber-12/bin/mmpbsa_py_energy failed with
prmtop 3MBP-c.top!
Exiting. All files have been retained.
There are other people posted similar situations in last year and people
replys that the MMPBSA.py code in amber12 had major modifications that they
wasn't sure what is going on. Therefore, I do think it is a problem in the
script not due to a specific system.
I will try to run my calculations with earlier amber version and let you
know my finding later.
Cheers,
WenJuan
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Received on Sun Feb 10 2013 - 21:30:03 PST
