Re: [AMBER] mmgbsa tricky output: PART 2

From: Amor San Juan <>
Date: Wed, 7 Jul 2010 03:03:10 -0700 (PDT)

Hi Jason,

Thanks for the explanation. In using the module 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.


--- On Tue, 6/7/10, Jason Swails <> wrote:

From: Jason Swails <>
Subject: Re: [AMBER] mmgbsa tricky output: PART 2
To: "AMBER Mailing List" <>
Date: Tuesday, 6 July, 2010, 9:00 PM


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 script, you can
use the "-make-mdins" flag to get the mdin files for your simulation.  If
you're using, you can search the file for
the mdin files used.

Hope this helps,

On Tue, Jul 6, 2010 at 2:48 AM, Amor San Juan <> 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

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Wed Jul 07 2010 - 03:30:03 PDT
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