Dear Prof. Hay,
Attached is "_MMPBSA_cpptraj_entropy.out" file.
The command for performing quasiharmonic calculation:
mpirun -np 6 MMPBSA.py.MPI -i nmode.in -cp com.prmtop -rp rec.prmtop -lp
lig.prmtop -y prod.binpos
For information, I performed MD production of the system contained solvated
receptor (protein, DNA, MG ions) and ligand.
And before performing quasiharmonic, I stript out all solvent and MG and
Na+ ions.
Thanks for your response.
Best!
nadaafiva
On Sun, Sep 10, 2017 at 10:52 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> detail commands + output would be really helpful. cheers
> Hai
>
> On Sat, Sep 9, 2017 at 10:50 PM, Nada Afiva <nadaafiva.gmail.com> wrote:
>
> > Dear all,
> >
> > I am performing quasiharmonic calculation for receptor-ligand complex.
> The
> > receptor contains protein, DNA, and MG ions.
> >
> > My input file was:
> >
> >
> > Input file
> >
> > &general
> >
> > Startframe=15000, endframe=20000, interval=500,
> >
> > Keep_files=2, entropy-1,
> >
> > /
> >
> >
> >
> > However, the calculation always failed with error “CalcError:
> > /home/amber16/bin/cpptraj failed with prmtop protein-ligand.prmtop!
> >
> > The error seems to be due to prmtop file, but I have performed entalphy
> > calculation using MMPBSA.py with the same prmtop file, and it run
> > successfully.
> >
> > So I am wondering how to solve that problem.
> >
> > Thansk so much for any comment suggestion.
> >
> >
> >
> > Best!
> >
> > nadaafiva
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> >
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Received on Sat Sep 09 2017 - 21:00:02 PDT
