I know little of the apbs-pymol integration, but in general, you can use the PROPKA support built into PDB2PQR to assign protonation at different pHs and then feed your pqr to apbs.
See http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr for the --with-ph option. There's also a whole different world of using apbs to determine pKa (see http://www.poissonboltzmann.org/apbs/examples/pka-calculations ) -David On Wed, Apr 7, 2010 at 12:49 PM, Soisson, Stephen M <stephen_sois...@merck.com> wrote: > Hi- > > Does anyone know if it is possible to calculate the charged surface using > apbs at different pHs? I am assuming the default pH is 7. > > Thanks in advance- > > Steve > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New > Jersey, USA 08889), and/or its affiliates Direct contact information for > affiliates is available at http://www.merck.com/contact/contacts.html) that > may be confidential, proprietary copyrighted and/or legally privileged. It > is intended solely for the use of the individual or entity named on this > message. If you are not the intended recipient, and have received this > message in error, please notify us immediately by reply e-mail and then > delete it from your system. > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > 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 > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
