[AMBER] ante-mmpbsa.py: troubleshooting

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 13 May 2015 20:26:36 +0200

I manage to successfully use ante-mmpbsa.py to create prmtop files for a homodimer in complex with two identical ligands. The ligands were not stripped from the dimer. I then successfully run mmpbsa.py.MPI.

My intention is to find out if the ligands affect deltaG binding. I’ve repeated the ante-mmpbsa.py process by stripping the ligands.
The script used is:

ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop -l subB.prmtop -s :DE3,:DE4,:WAT,Na+ -m :1-125 --radii=mbondi2

The prmtop files produced seem to be in order.

1. cpptraj subA.prmtop
parminfo Topology subA.prmtop contains 1992 atoms.
                                  125 residues.
                                  2023 bonds.
                                  1 molecules.
                                  Box: None
2. cpptraj subB.prmtop
parminfo Topology subB.prmtop contains 1992 atoms
3. cpptraj subA-subB.prmtop
parminfo Topology subA-subB.prmtop contains 3984 atoms.
                                  250 residues.
                                  4046 bonds.
                                  2 molecules.
                                  Box: None

I then run mmpbsa.py using the following script:

mpirun -np 12 MMPBSA.py -O -i decomp.in -o FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP__MMPBSA.dat -sp complex_solv.prmtop -cp subA-subB.prmtop -rp subA.prmtop -lp subB.prmtop -y *.nc

It runs up to a point and then aborts issuing the following message:

Beginning GB calculations with /Users/gtzotzos/Programs/MD/amber12/bin/sander
  calculating complex contribution...
CalcError: /Users/gtzotzos/Programs/MD/amber12/bin/sander failed with prmtop subA-subB.prmtop!
Exiting. All files have been retained

I’d appreciate any suggestions how to troubleshoot this.

Thanks in advance


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Received on Wed May 13 2015 - 11:30:04 PDT
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