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.moustafa@...>: 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=
> ------------------------------------
>
>
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>
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> correo-e: ibdeno@...
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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/
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