Hi Andrew, The main limitation for problems like this is that you need to have parameters for the ligand. Making sure that you have "good" parameters is often an expert-level topic, and you're probably best served by the APBS or PDB2PQR listservs as well as the literature ... but, you can get a decent start on things with PDB2PQR itself. See http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization for some good starting instructions. Once you have a PQR file that includes both the protein and the ligand, the PyMOL/APBS plugin should do everything that you need.
If that doesn't solve your problem, please let me know. Cheers, -Michael On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew <andrew.mal...@umassmed.edu> wrote: > Hey guys, > > I am trying to calculate electrostatics with a ligand bound to my molecule > using ABPS. I am not having success. Everything I've read seems to say that > this is a normal limitation with APBS, and I've tried other programs to no > avail. I have not been able to rebuild my molecule in the "correct format" > either. Any help here is greatly appreciated. > > Andrew > UMass Med School, Worcester, MA > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 ------------------------------------------------------------------------------ Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
