> On May 13, 2015, at 2:26 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
> 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
Isn't this the same problem in your last email? You are using mpirun for a serial simulation?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 13 2015 - 12:30:02 PDT
