I have experience with APBS. PyMol has an APBS plugin. You can also use APBS using AutoDock Tools (http://autodock.scripps.edu/resources/adt) However, I suggest that you visit first the APBS website. There's plenty of information there (http://www.poissonboltzmann.org/apbs/) Regards George On Jun 26, 2012, at 3:48 PM, cantini@cerm.unifi.it wrote:

Regarding these programs Do you know how they worked and which are the best? I tried to installed them but without success .

Francesca

sette@uniroma2.it ha scritto:

...

Chimera don't make calculations of electrostatic potential. You can use other softwares for this, like APBS or Delphi.

Marco

George Tzotzos <gtzotzos@me.com> ha scritto:

...

Hi everybody,

Assuming that one knows the precise residues constituting a binding site, it is possible to calculate the electrostatic potential of these residues only? If yes, how?

Thanks for any advice

George _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328

www.rete29aprile.it

---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Marco, Many thanks. I'm aware of the APBS type of calculation, but Chimera provides Coulombic Surface Coloring. See file:///Applications/Chimera.app/Contents/Resources/share/chimera/helpdir/ContributedSoftware/coulombic/coulombic.html However, I'm a bit confused by the description. I quote "The molecular surface(s) should first be displayed (using Actions... Surface... show or the command surface) and then chosen from the list of Surfaces to color by ESP" Following this routine works but does not provide a list of "Surfaces to color by ESP". Probably one has to generate first a grid by the Compute grid option. Somehow, I cannot see how this option is activated from the Volume Viewer. Best regards George On Jun 26, 2012, at 3:12 PM, sette@uniroma2.it wrote:

Chimera don't make calculations of electrostatic potential. You can use other softwares for this, like APBS or Delphi.

Marco

George Tzotzos <gtzotzos@me.com> ha scritto:

...

Hi everybody,

Assuming that one knows the precise residues constituting a binding site, it is possible to calculate the electrostatic potential of these residues only? If yes, how?

Thanks for any advice

George _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328

www.rete29aprile.it

---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Elaine, Many thanks. My mistake. I was looking at the Electrostatic instead of the Coulombic Surface Coloring. Apologies. Best regards George On Jun 26, 2012, at 6:40 PM, Elaine Meng wrote:

Hi George, I'm confused by the confusion. That sentence merely says you need to show a surface first, or else there will be nothing to color. You do not need to make a grid beforehand (or ever) to use Coulombic Surface Coloring. Grid output is just an option of Coulombic Surface Coloring.

Whether you use Coulombic ESP or some outside program (APBS, DelPhi etc.) to calculate ESP, you could of course delete all of the other atoms before the calculation if you really only want the potential to be calculated from part of the structure.

However, in my opinion, just chopping away part of the structure would not be meaningful because electrostatics are rather long-range, and at least for the Poisson-Boltzmann calculations the ESP value at any point depends also on the distribution of low-dielectric (buried) and high-dielectric (aqueous solvent) regions in space. Instead you probably want to calculate the atoms' or residues' contribution to the total electrostatic energy of the system, or to the electrostatic interaction with some other molecule. This would require more complicated calculations probably involving a thermodynamic cycle. Please consult the literature and the manuals of those other programs (APBS) etc. if you want to get into that area.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 26, 2012, at 6:49 AM, George Tzotzos wrote:

...

Hi Marco,

Many thanks. I'm aware of the APBS type of calculation, but Chimera provides Coulombic Surface Coloring. See file:///Applications/Chimera.app/Contents/Resources/share/chimera/helpdir/ContributedSoftware/coulombic/coulombic.html

However, I'm a bit confused by the description. I quote "The molecular surface(s) should first be displayed (using Actions... Surface... show or the command surface) and then chosen from the list of Surfaces to color by ESP"

Following this routine works but does not provide a list of "Surfaces to color by ESP". Probably one has to generate first a grid by the Compute grid option. Somehow, I cannot see how this option is activated from the Volume Viewer.

Best regards

George

On Jun 26, 2012, at 3:12 PM, sette@uniroma2.it wrote:

...

Chimera don't make calculations of electrostatic potential. You can use other softwares for this, like APBS or Delphi.

Marco

George Tzotzos <gtzotzos@me.com> ha scritto:

...

Hi everybody,

Assuming that one knows the precise residues constituting a binding site, it is possible to calculate the electrostatic potential of these residues only? If yes, how?

Thanks for any advice

George _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328

www.rete29aprile.it

---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users