RE: [AMBER] Stability Calculation Using

From: Hopkins, Robert <>
Date: Thu, 29 Apr 2010 15:24:31 -0500

Thanks Jason!


From: on behalf of Jason Swails
Sent: Thu 4/29/2010 2:49 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Stability Calculation Using

Hi Bob,

We did not add this capability to 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
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 <> wrote:

> Amber/MMPBSA Developers and Users,
> It doesn't appear that 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
> Thanks!
> Bob Hopkins
> _______________________________________________
> AMBER mailing list
All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Thu Apr 29 2010 - 13:30:04 PDT
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