Re: [AMBER] QM/MM MMPBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 4 Oct 2013 09:59:18 -0400

On Fri, Oct 4, 2013 at 9:53 AM, Jason Swails <jason.swails.gmail.com> wrote:

>
>
>
> 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
>

OK, I attached another patch. Please apply it the same way as the last one
and test this.

cd $AMBERHOME
./update_amber --apply mmpbsa.patch2
make -C $AMBERHOME/AmberTools/src/mmpbsa_py install

Thanks!
Jason


>
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>



-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher



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Received on Fri Oct 04 2013 - 07:00:22 PDT
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