On Fri, Oct 4, 2013 at 8:15 AM, Jacopo Sgrignani <sgrigna.gmail.com> wrote:
> Dear Jason
> thanks for the patch. It works well and solved the problem.
>
The patch should also fix -use-mdins with QM/MM input files.
Thanks again for the report, I'll push this forward as an update.
--Jason
>
> Jacopo
>
> Inviato da iPad
>
> > Il giorno 04/ott/2013, alle ore 13:07, Jason Swails <
> jason.swails.gmail.com> ha scritto:
> >
> >> On Fri, Oct 4, 2013 at 4:18 AM, Jacopo Sgrignani <sgrigna.gmail.com>
> wrote:
> >>
> >> Dear all
> >> I'm trying to run MMPBSA Qm/MM calculations but I have some problems:
> >>
> >> 1) Even though I define ligand, receptor and complex qm-charge the
> >> program ignores these numbers and the qm-charge unspecified in the
> >> generated inputs file.
> >>
> >> 2) To overcome the first problem, I tried to use -make-mdins and then
> >> -use-mdins putting the charge in the generated files.
> >> However when I use the -use-mdins command the existing inputs are
> >> automatically deleted.
> >> I'm using my personal workstation so I can exclude automatic cleaning
> >> procedure.
> >>
> >> Can you help me?
> >
> > I was able to reproduce your problem, and I have a solution that appears
> to
> > work. Please apply the attached patch, rebuild MMPBSA.py, and try again.
> > The following steps should do everything (assuming you put mmpbsa.patch
> in
> > $AMBERHOME):
> >
> > cd $AMBERHOME
> > ./update_amber --apply mmpbsa.patch
> > make -C AmberTools/src/mmpbsa_py install
> >
> > That should reinstall MMPBSA.py without spending time rebuilding the rest
> > of Amber (which this patch does not affect).
> >
> > If this patch works, I will roll it out as an update.
> >
> > Thanks for the report!
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > <mmpbsa.patch>
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 04 2013 - 06:00:20 PDT
