[Chimera-users] Residue selection for simulation/energy-minimization

[Kim, In-Kwon (kimiw)]

Dear,
I am trying to publish our structure and modeling done by CHIMERA.
My questions are

  1.  What is the default option for distance for selecting residues around ligand (e.g., XX A around ligand).
  2.  Any time scale for simulation?

Here is my method description. Any suggestion, related citation, and help would be appreciated.

“~. Residues within XX A of the ligand was selected for simulation. The model was then subjected to energy minimization using the AMBER ff14SB protein force field in the Chimera package (34).”

Thanks,

In-Kwon


In-Kwon Kim, Ph.D.
Assistant Professor
Department of Chemistry
University of Cincinnati
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