[Chimera-users] energy optimization of the modle from homology modeling

aixintiankong aixintiankong at 126.com
Sat May 11 18:50:11 PDT 2013

   i am a newer use the chimea, i have some question to consult to you, please help me.

  Frist, after Homology modeling using the chimera modeller, should i optimizate the modle by energy optimization or Molecular dynamic simulations? The next step i will use the model to make docking.
  Second, i want to use chimera to minimize the structrue of my modle.   i select Tools>Structure Editing>Minimize Structure to perform my work, but my modle include protein and a organic molecule NAD+, so i don't know how to select the force fileds for the minimiztion of the modle. please help me.
  Third, if i olny want to use the conjugate gradient to perform the minimiztion, should i only need to set the steepest descent steps to 0?  in general, how many conjugate gradient steps and size should be ?
  Thank you very much!
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