Hi George,
You will need to provide MMPBSA.py the following:
mpirun -np 48 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
-sp {solvated complex prmtop} -srp {solvated receptor prmtop} -slp
{solvated ligand prmtop} -cp { dry complex prmtop} -rp
{ dry receptor prmtop} -lp { dry ligand prmtop} -y {complex traj} -yr
{receptor traj} -yl {ligand traj}
HTH,
Dwight
On Wed, Oct 21, 2015 at 12:10 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you Dwight
>
> I tried your suggestion as follows:
>
> mpirun -np 48 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
> -slp lig_solv.prmtop -lp lig.prmtop -yl *.nc
>
> mmpbsa throws the following error:
>
> IOError: Could not open complex_prmtop for reading
> Error occured on rank 1
> Any suggestions?
>
> George
>
> > On 21 Oct 2015, at 18:53, Dwight McGee <dwight.mcgee.gmail.com> wrote:
> >
> > Hi,
> >
> > If you are using the triple trajectory approach, the flags for the ligand
> > are *-yl* {ligand solvated traj} and *-slp* {ligand solvated prmtop}.
> >
> > Regards,
> > Dwight
> >
> > On Wed, Oct 21, 2015 at 11:19 AM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >
> >> I’m trying to compare the delta-G of binding of a complex using the
> >> single- and three-trajectory approach.
> >>
> >> In the single trajectory approach, as per manual, th command used was:
> >>
> >> mpirun -np 48 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
> >> -sp cmplx_solv.prmtop -cp cmplx.prmtop -rp rec.prmtop -lp lig.prmtop -y
> *.nc
> >>
> >> To get a more accurate estimate of the desolation parts of the energy of
> >> the receptor and ligand, I’m trying to use the three trajectory
> approach. I
> >> have run separate trajectories of the complex and one of the subunits.
> >>
> >> I looked at the manual but could not find an appropriate flag for the
> >> solvated ligand file.
> >>
> >> I’d be grateful for any advice on the correct usage.
> >>
> >> Regards
> >>
> >> George
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > T. Dwight McGee Jr.
> >
> > dwight.mcgee.gmail.com
> >
> > "Problems cannot be solved at the same level of awareness that created
> > them."
> > Albert Einstein
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Wed Oct 21 2015 - 10:00:04 PDT
