Thanks - Vina is being used, and if all H are not added before energy minimization, it appears that results are off (e.g. long CH2 chains will look like a loose rope). Yes, Vina only leaves polar H in the resulting pdbqt files.
Get Outlook for Android On Sat, Nov 3, 2018 at 6:38 AM -0500, "Maciek Wójcikowski" <mac...@wojcikowski.pl> wrote: Hi, This is highly dependent on docking software. Autodock Vina requires only polar hydrogens, but others will differ. Best, Maciek sob., 3 lis 2018, 11:28: Noel O'Boyle <baoille...@gmail.com> napisał(a): You need to add all hydrogens. I have never understood why those options are provided. On Thu, 1 Nov 2018, 19:41 Leif Peterson <leifepeter...@sbcglobal.net wrote: Before performing ligand energy minimization then docking with receptors, I am adding hydrogens to ligands via the syntax: Addhydrogens(False, False); I am pretty sure this adds implicit H since polar-only is false. For docking, should I only add polar H, or is ...(False, False) the recommended choice for ligand prep? _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
