Hi Joel, Try this:
1) Click on "Builder" (upper right quick buttons) 2) Click "Charge: +1" 3) Click on the nitrogen atom This should put a positive charge (formal_charge) on the nitrogen and also add hydrogens to fill open valences. To add hydrogens to all atoms, click "Add H". Command line equivalent: PyMOL> alter name N, formal_charge=1 PyMOL> h_add Cheers, Thomas > On Mar 20, 2018, at 2:13 AM, Joel Tyndall <joel.tynd...@otago.ac.nz> wrote: > > Hi folks, > > Is pymol able to protonate an amine e.g. morphine i.e. when you add hydrogens > to a small molecule, ensure that the amine is charged (at it would be at > physiological pH? > > I have not been able to do it using the GUI. > > Cheers > > Joel > > Joel Tyndall | BSc(Hons) PhD > > Associate Professor in Medicinal Chemistry > School of Pharmacy | Te Kura Mātauraka Wai-whakaora > University of Otago | Te Whare Wānanga o Otāgo > PO Box 56 9054 > Dunedin | Ōtepoti > New Zealand | Aotearoa > Ph: 64 3 479 7293 > Skype: jtyndall > Website | pharmacy.otago.ac.nz -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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
