Hi JW,

OK, I see. In this case, it is probably better to have separate pqr files (protein and ligand) and run apbs plugin twice in PyMOL, so that you can visualize them separately.

Thanks,

Yong


On Fri, Jun 18, 2010 at 11:52 AM, JW Feng <feng.jw@gene.com> wrote:
Hi Yong,

My first tries were using complex.pqr and running apbs just once, but I could not visualize just the ligand surface or just the protein surface. What I got seems to be a mixture of the two surfaces. Maybe I am not interpreting the data correctly.

JW
-------------------------------------------------------------------
JW Feng Ph.D.
Computational Chemistry and Cheminformatics
Genentech, Inc.
-------------------------------------------------------------------
Tel: 650-225-4529
Fax: 650-467-5155
feng.jw@gene.com
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On Fri, Jun 18, 2010 at 8:12 AM, Yong Huang <yhuang01@gmail.com> wrote:
Hi JW,

What you described here should work. Alternatively, you can load complex.pqr (the output from PDB2PQR, with both protein and ligand) in PyMOL, then run apbs plugin job just once, and then visualize.

Good luck,

Yong



On Thu, Jun 17, 2010 at 11:57 PM, JW Feng <feng.jw@gene.com> wrote:
Hi Nathan,

How do you generate a pqr file for the ligand molecule? I used the --ligand=ligand.mol2 option in pdb2pqr.py to create a pqr file that contains records for both protein and ligand. I then split that pqr file into a ligand.pqr file which contains† HETATM records and a protein.pqr file which contains ATOM record. Next, I loaded the protein-ligand complex as a single PDB file into PyMOL. I then ran two apbs calculations using the apbs plugin in PyMOL, one for ligand.pqr and another for protein.pqr. Is this a right way to visualize electrostatic complementarity between the ligand and protein?

Thanks,

JW
-------------------------------------------------------------------
JW Feng Ph.D.
Computational Chemistry and Cheminformatics
Genentech, Inc.
-------------------------------------------------------------------
Tel: 650-225-4529
Fax: 650-467-5155
feng.jw@gene.com
-------------------------------------------------------------------


On Thu, Jun 17, 2010 at 7:45 PM, Baker, Nathan <Nathan.Baker@pnl.gov> wrote:

Hi JW Ė

I just calculated the electrostatic potential for the isolated balanol and then displayed it superimposed on the PKA structure.† The PKA structure didnít influence the calculation of the balanol potential.

Good to hear from you!

Nathan

From: JW Feng [mailto:feng.jw@gene.com]
Sent: Thursday, June 17, 2010 2:52 PM
To: apbs-users@lists.sourceforge.net
Subject: [Apbs-users] Isosurface for ligand molecules

Hi Nathan and APBS Users,

On slide 57 of your presentation that was given at the NBCR workshop, you showed an image of protein kinase A inhibited by balanol. How did you generate the isosurface for balanol?† I am interested in using apbs to calculate electrostatic surface of a ligand and see how it complements the electrostatic surface of the receptor binding pocket.

Thanks,

JW

-------------------------------------------------------------------
JW Feng Ph.D.
Computational Chemistry and Cheminformatics
Genentech, Inc.
-------------------------------------------------------------------
Tel: 650-225-4529
Fax: 650-467-5155
feng.jw@gene.com
-------------------------------------------------------------------



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--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine




--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine