Thanks Jason!
Bob
________________________________
From: amber-bounces.ambermd.org on behalf of Jason Swails
Sent: Thu 4/29/2010 2:49 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Stability Calculation Using MMPBSA.py?
Hi Bob,
We did not add this capability to MMPBSA.py. We didn't see the need to add
that capability in, since it can be done in a single step without using a
script using imin=5 (trajectory analysis) in sander. You can have MMPBSA.py
create the mdin files and run the simulation with that if you'd like.
On Thu, Apr 29, 2010 at 3:36 PM, Hopkins, Robert <hopkins.uhcl.edu> wrote:
> Amber/MMPBSA Developers and Users,
>
> It doesn't appear that MMPBSA.py is set up to simply estimate the free
> energies of two nearly identical structures for comparison of their
> stabilities (no binding involved). Since the Perl scripts had this
> capablility, I tried using only the prmtop data for the receptor, but the
> Python script complained! So, is it possible to do this type of calculation
> using MMPBSA.py?
>
> Thanks!
> Bob Hopkins
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Apr 29 2010 - 13:30:04 PDT
