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
etc.
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
George
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 13 2015 - 11:30:04 PDT
