ADL: Could anyone help me please??

Stefano Forli forli at scripps.edu
Fri Nov 18 14:33:27 PST 2011


Hi Normandé,

I agree with Mihaly's hypothesis, especially if an MD is involved.
Another thing thing that could help you to 'sanitize' a bit the input PDB could be to 
pre-process the file with OpenBabel, with PDB as both input and output format. Sometimes 
this helps to fix atom name misalignments and/or exotic naming conventions.

Hope this helps,

Stefano

On 11/18/2011 02:30 PM, Mihaly Mezei wrote:
> Hi,
>
> your molecule probably was distroted at a few places, so some bonds appear to be broke and that confuses ADT. Try a short minimization of the final structure and see it ADT likes it better.
>
> Mihaly Mezei
>
> Department of Structural and Chemical Biology, Mount Sinai School of Medicine
> Voice:  (212) 659-5475   Fax: (212) 849-2456
> WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
> WWW (Department): http://atlas.physbio.mssm.edu
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---


-- 
  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-112
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

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


More information about the autodock mailing list