Re: [AMBER] MM-PBSA for membrane protein system

From: Ray Luo via AMBER <amber.ambermd.org> Date: Wed, 20 Mar 2024 08:07:10 -0700

--
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 Wed, Mar 20, 2024 at 5:45 AM Bhattacharjee, Sinjini via AMBER <
amber.ambermd.org> wrote:
> Hello all,
>
> I want to perform a MM-PBSA calculation for a membrane-protein system
> using the following input. How do I estimate the mctrdz and mthick from the
> MD trajectory? Can this be done using cpptraj or do I need an external
> program? Any help would be appreciated.
>
> &general
> use_sander=1,
> startframe=1, endframe=3000, interval=10,
> keep_files=2, debug_printlevel=2
> /
>
> &pb
> radiopt=0,
> indi=20.0,
> istrng=0.150,
> fillratio=1.25,
>  ipb=1,
> nfocus=1,
> bcopt=10,
> eneopt=1,
> cutfd=7.0,
> cutnb=99.0,
> npbverb=1,
> solvopt=2,
> inp=1,
> memopt=1,
> emem=7.0,
> mctrdz=0.0,
> mthick=36.086,
> poretype=1,
> maxarcdot=15000
> /
>
>
> Thanks and best regards,
>
> —
> Sinjini Bhattacharjee
>
> PhD Student
> Molecular Theory and Spectroscopy
> Max-Planck-Institut für Kohlenforschung
> 45470 Mülheim an der Ruhr, Germany
>
> email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>
> ---
>
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