Thanks Jason,
No, I’m not using serial. I recompiled the whole lot.
mmpbsa.py.MPI now runs properly. I’ve already run it successfully once after generating prmtop files via ante-mmpbsa.py (see the 1st sentence of my email below).
That’s why I’m in the dark now.
George
> On 13 May 2015, at 21:19, Jason Swails <jason.swails.gmail.com> wrote:
>
>
>
>> 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 - 12:30:03 PDT
