HI Francesco, It is probably that the automatic atom-type identification does not assign the type that you wanted, maybe because it is difficult to tell from the atomic coordinates. Atom types are listed here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html> The workaround is simply to change the atom type to sp3 carbon right before adding hydrogens. In your case, in the model from the pdbqt file, select just the carbon whose type you want to change (Ctrl-click) and then use command setattr a idatmType C3 sel Or, instead of “sel” to specify the selected atom(s), you can specify by name, for example if it was atom C12 in residue DTP: setattr a idatmType C3 :DTP@C12 You can label to show atom type. Example commands to label the selected atoms: labelopt info idatmType label sel The labels will not change automatically, so if you showed these labels before changing the type, you have to show labels again (using command or menu) to show the new type. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2017, at 12:15 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
pdbqt from autodock-vina -> pdb with chimera -> addH with chimera.
Chimera fails (systematically) to add one H to a quaternary carbon of the diterpenoid.
avogadro (which does not understand pdbqt) does the addH job correctly from chimera-savedpdb.
Should Eric be interested, I could send (privately) the file
best regards
francesco pietra