Re: [AMBER] the parameter mctrdz in mmpbsa.in

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Wed, 13 Sep 2023 17:06:53 -0700

Shiyu,

The program can only figure out the center of the full protein as
inputted, not that of the membrane domain since there is no way to
tell the program which is which.

So for your case, you'd better specify the center via input.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Tue, Sep 12, 2023 at 8:29 PM shiyu wang via AMBER <amber.ambermd.org> wrote:
>
> Dear all:
>
>
> I am calculating the binding energy of membrane protein and its ligand
> via MMPBSA.py.
>
>
> However, in the AMBER manual file, the parameter mctrdz means is
> explained "Membrane center in Å in the z direction. Default is 0 -
> membrane centered at the center of the protein."
>
>
> My question is : "the center of the protein" means "the center of the
> whole protein" or "the center of the trans membrane domain of protein"?
>
>
> thank you.
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Received on Wed Sep 13 2023 - 17:30:02 PDT
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