Re: [AMBER] Fwd: [Sender Not Verified] Electrostatic potential calculation of the active site

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Mon, 26 Jun 2023 08:16:15 -0700

Hi Mondal,

Potential values can be printed out and visualized with Amber/PBSA.
See the chapter on PBSA on its visualization function in the Amber
manual. You can choose the commonly used xml format for easy
processing.

However, printing potential at a specific location is not supported.
If you know the coordinates, you can interpolate the values at these
residue locations using the potential values at their nearest grid
points. The simplest approach would be to use the 8 nearest grid
points and the trilinear approach. You can use more points and
higher-order methods as well.

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 Mon, Jun 26, 2023 at 4:04 AM Dulal Mondal via AMBER
<amber.ambermd.org> wrote:
>
> Dear Experts,
>
> Thanks for your reply.
> I have used APBS in VMD to plot electrostatic potential surface. But I am
> trying to calculate the potential value.
>
> ---------- Forwarded message ---------
> From: Steinbrecher, Thomas <thomas.steinbrecher.roche.com>
> Date: Mon, 26 Jun, 2023, 4:14 pm
> Subject: Re: [Sender Not Verified] [AMBER] Electrostatic potential
> calculation of the active site
> To: Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
>
>
> Hi Dulal,
>
> Im not an expert on electrostatics calculations, but I think you'd have to
> be more precise in your question to get a meaningful answer on this mailing
> list. What exactly are you trying to calculate and what did you try so far?
>
> Kind Regards,
>
> Thomas
>
> On Mon, Jun 26, 2023 at 12:28 PM Dulal Mondal via AMBER <amber.ambermd.org>
> wrote:
>
> > Dear Users,
> >
> > I have a protein system. I am trying to calculate some selected residues'
> > total electrostatic potential values (like Tyr-7, His-94, and His-96). How
> > can I calculate the electrostatic potential value?
> >
> > Thanking you in advance
> > *With regards,*
> > *Dulal Mondal,*
> > *Research Scholar,*
> > *Department of Chemistry,*
> > *IIT Kharagpur, Kharagpur 721302.*
> > _______________________________________________
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> >
>
>
> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
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Received on Mon Jun 26 2023 - 08:30:02 PDT