On Fri, Oct 4, 2013 at 9:33 AM, Jacopo Sgrignani <sgrigna.gmail.com> wrote:
> Dear Jason
> I'm sorry to write another email but my colegues noted that, while in the
> MMPBSA.in file the qm charges are specified without decimal numbers (i.e. 1
> 2 3) the script produces input files with decimal numbers (1.0 2.0 etc..).
> So we are able to run the calculations only manually editing the mdins
> files, because it seems that sander does not like decimal numbers in the
> input file.
>
Ugh. OK, I'll fix that. Thanks
Jason
>
> Thanks again
>
> Jacopo
>
> > Il giorno 04/ott/2013, alle ore 14:34, Jason Swails <
> jason.swails.gmail.com> ha scritto:
> >
> >> 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>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> >
> >
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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 - 07:00:06 PDT
