Re: [Apbs-users] calculating dipole moment

[Nathan B. <sob...@gm...>]

Hi Miguel --

This sounds like a great tool; APBS doesn't have any direct user-=20
accessible way to calculate this (either from the charge distribution =20=

or from the electrostatic potential) at this time.

Thanks!

-- Nathan

On Jun 2, 2007, at 5:22 AM, Miguel Ortiz-Lombard=EDa wrote:

> Hi Ibrahim,
>
> I wrote recently a python script that just do so. I had planned to =20
> learn how to integrate it as a pdb2pqr extension, but have not =20
> found the time yet. I'm attaching it to this post in case someone =20
> finds it useful and is willing to do so ;-)
>
> This is what the script does:
>
>   dipole.py
>
>   Script based on pdb2pqr to calculate the dipole moment of a protein
>   It either takes a pdb or a pqr file. In the former case, it runs
>   pdb2pqr using the force field selected by the user.
>   If a pqr file the dipole calculation is made directly from this =20
> file.
>   The dipole is calculated with origin at the charges-weighted centre
>   of the protein. This is the convention when the molecule is not =20
> neutral.
>
>   It produces a bild file that can be read by the program Chimera
>   (http://www.cgl.ucsf.edu/chimera/) to represent the dipole moment =20=

> vector
>   The user can select an appropriated color, or green will be used
>
>   Much of the code to interface with pdb2pqr is actually from pdb2pqr,
>   by Todd Dolinsky, Nathan A. Baker et al.
>
>   Added some bits to deal with proteins that contain Se-Met (MSE)
>   amino acids.
>
>   Miguel Ortiz-Lombardia 21/03/2007
>
> In case you don't use chimera, you can read the charge-weighted =20
> centre of the molecule and the coordinates of the dipole moment, so =20=

> you can display the vector in your favourite graphics program.
>
> I hope you find it useful.
>
> Cheers,
>
>
> Miguel
>
> 2007/6/1, Ibrahim M. Moustafa <I.m...@ps...>: Dear users,
>
>     I want to calculate the dipole moment of few proteins to compare
> and want to be able to visualize it; something similar to what =20
> GRASP does.
> I'm wondering if I can do that in APSB?!.
>
>    thanks,
>   Ibrahim
>
>
> ----------------------------------------------------------------------=20=

> ------------------------------------
> Ibrahim M. Moustafa, Ph.D.
> Biochemistry and Molecular Biology Dept.
> 201 Althouse Lab., Uinversity Park
> Pennsylvania State University, PA16802
>
> Tel.  (814)863-8703
> Fax. (814)865-7927
> ----------------------------------------------------------------------=20=

> ------------------------------------
>
>
> ----------------------------------------------------------------------=20=

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> --=20
> correo-e: ib...@gm...
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~=20=

> ~
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>                                            Georges Brassens
> <dipole.py>
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--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/