Dear,

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 s! teps and size should be ?

Thank you very much!