Hello,
I'm not talking about using the module alone. In order to do that, I think
you'd have to create another perl script that called that file (since it's a
perl module). I don't use perl (I prefer python), so I don't exactly know
the ins and outs of that language. I'm talking about opening that file with
a text editor and actually going through the script to find where that input
file is being written and using that.
Good luck!
Jason
On Wed, Jul 7, 2010 at 6:03 AM, Amor San Juan <amorsanjuan.yahoo.com> wrote:
> Hi Jason,
>
> Thanks for the explanation. In using the module mm_pbsa_createinput.pm to
> obtain mdin file, did you have the experience using this module alone? I
> search the manual but coudnt find info how to use this module as standalone
> executable.
>
> Amor
>
> --- On Tue, 6/7/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] mmgbsa tricky output: PART 2
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Tuesday, 6 July, 2010, 9:00 PM
>
> Hello,
>
> I believe what was meant was that you should extract a single frame and run
> all of the MM/GBSA calculations on it to see what value your get for the
> binding free energy. If you're trying to use the MMPBSA.py script, you can
> use the "-make-mdins" flag to get the mdin files for your simulation. If
> you're using mm_pbsa.pl, you can search the file mm_pbsa_createinput.pmfor
> the mdin files used.
>
> Hope this helps,
> Jason
>
> On Tue, Jul 6, 2010 at 2:48 AM, Amor San Juan <amorsanjuan.yahoo.com>
> wrote:
>
> > As posted previously, I face result of mmgbsa with a large value of -1600
> > kcal/mol. I received suggestion that "If the trajectories are okay, you
> > might want to use one snapshot to
> > run the job by hand to find out why ..."
> >
> > Can anyone here kindly inform me how to make a snapshot run by hand? I
> took
> > the generated snapshot from the complex and now for me to run a
> production,
> > I need to put water molecules in a box. Does this mean I will use leap to
> > add water and perform minimization and heating again prior running a
> > production.
> >
> > Amor
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jul 07 2010 - 07:30:03 PDT
