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.pm for
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
>
>
>
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>
--
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 - 03:30:03 PDT
