Parametarization and geometry optimization

From: Dhiraj Srivastava (
Date: Tue Nov 20 2012 - 07:26:35 CST

  I am trying to develop Charmm parameter for my cofactor. While doing
geometry optimization by Gaussian, the Cofactor is going from the bend
conformation (from Crystal structure) to extended conformation. Now my
question is, the cofactor in my protein is in bend conformation and the
parameter I am developing is for extanded conformation, So is it ok to use
the parameter for extended conformation into my simulation?

Thank you

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:46 CST