ADL: prepare_ligand4py fails on quaternary nitrogen atoms

Stefano Forli forli at scripps.edu
Mon Dec 8 16:28:59 PST 2014


Brian,
it would be helpful if you could provide an example of such molecules and a description of 
what the specific issue is (e.g. unrecognized rotatable bonds, misplaced hydrogens, etc...).

Without a well-defined structure it is hard to help, but a general advice for peculiar 
molecular structures is to add hydrogens using tools that are more sophisticated than 
AutoDockTools (that's known to have problems with some nitrogen-containing structures), 
then generate the PDBQT file with the scripts or the graphical interface.

S


On 12/08/2014 04:24 PM, Bennion, Brian wrote:
>
> ________________________________
>
>
> Hello,
>
> I am wondering if there is a way to help prepare_ligand4.py recognize and properly prepare ligands for docking when they contain a quaternary nitrogen in which two bonds are part of a 6 member ring.
>
> Brian
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>

-- 
  Stefano Forli, PhD

  Staff Scientist
  Molecular Graphics Laboratory
  Dept. of Integrative Structural
   and Computational Biology, MB-112F
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: +1 (858)784-2055
     fax: +1 (858)784-2860
     email: forli at scripps.edu
     http://www.scripps.edu/~forli/


More information about the autodock mailing list