Re: [AMBER] Using PBSA to Calculate Solvation Free Energy

From: Ray Luo <rluo.uci.edu>
Date: Mon, 25 Apr 2016 15:56:49 -0700

Dear Jiaqi,

You can use the sample input file in
$AMBERHOME/AmberTools/test/pbsa_dmp/Run.dmp.sasopt0 to do a quick
estimation.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Apr 25, 2016 at 3:31 PM, Jiaqi Jin <jiaqi.jin90.gmail.com> wrote:
> Dear all,
>
> I am interested in calculating the solvation free energy of a molecule in
> aqueous phase. I found from the Amber Manual that the PBSA module can be
> used for this calculation. I am able to build the topology and coordinates
> file about a molecule in a water box. However, I don't have the mdin file
> for running PBSA. Can anyone share your mdin file for calculating the
> solvation free energy using PBSA so that I can use as a reference? Thank
> you!
>
> Regards,
> Jiaqi Jin
> Metallurgical Engineering
> University of Utah
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Received on Mon Apr 25 2016 - 16:00:04 PDT
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