[Dock-fans] Re: running sphgen with cofactors

Le Tien Dung letiendzung at yahoo.com
Tue Oct 31 10:17:13 PST 2006

  This I have done quite a long time and almost forgot it.
  As far as I remember, I made a trick with the program.
  Firsly I removed the cofactor (mine is not a metal) then run DMS, the resulting surface file is then used for SPHEREGEN to calculate outer spheres
  After I get the spheres I convert into PDB format and view it with Deep View together with the original PDB file of the structure which contain the cofactor. With this I can identify the spheres that make clashes with the cofactor (since I removed the cofactor, there is potential that some spheres are generated in the place of the cofactor which is "un-real"). I removed all these spheres manually by opening the spheres file in a text editor. 
  In fact while doing this I could see only few spheres that clash, since my cofactor only is only close to the docking site, but not in the docking site.
  I am not sure if the same can be aplied with the metal cofactor, as far as I know J. Irwin has a paper on Biochemistry dealing with metallo enzymes, you may want to ask him.
  I am CC this mail to the docfan list in order to get critics if this trick is fundamentally wrong.
  Thank you for your e-mail
  Best wishes
  Dzung Le
Sameer Kawathar <sameer at ccrc.uga.edu> wrote:
    BODY{font:10pt Tahoma, Verdana, sans-serif;}    Hi,
  I saw you question on DOCK-fans about running sphgen with cofactors. Did you get any answers for that. I am having the same problem. My target contains calcium ion in the active site and the error message returned is the same as yours. Please reply me back. Any help is highly appreciated.
  Thank you,

                Le Tien Dung
  Postdoctoral fellow
  Department of Biochemistry & Redox Biology Center
  University of Nebraska-Lincoln
  N154, Beadle Center for Biomaterials
  Lincoln, NE 68588, USA
  Phone: (402) 472-4948
  E-mail: dle3 at unl.edu / To cellphone: 4023268702 at message.alltel.com 

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