how to set up force parameters of a novel residue?

From: He Yuhui (
Date: Thu Aug 27 2009 - 02:37:12 CDT

Dear all,

  I am now trying to simulate the motion of a guanine (G) base adhered
to Au electrodes via sulfur atom, i.e, some bond structure as follows:

  Therefore, I have to find bond, angle and dihedral parameters related
to this novel residue, e.g., Kb for Au-S bond, Ktheta for Au-S-N angle,
and so on.

  With Dr. Branko's suggestion, I have read the force-field tutorial. It
seems that I should do some quantum chemistry calculation of this
"molecule", and then extract those force-field parameters.

  Now it comes my question: tutorial of MOPAC (or GAMESS) tells that it
can calculate force parameters of a molecule system. I guess what it
presents are the normal modes of molecule vibration. How can I
"translate" these normal modes to force parameters?
  I am not clear of it, since normal modes are presented in generalized
coordinates while Kb, Ktheta and Kphi are related with localized atoms.

  Besides, I found the following description in intro of GAMESS:
  "The numerical force constant computation and normal mode analysis was
adapted from Andy Komornicki's GRADSCF program, with decomposition of
normal modes in internal coordinates written at NDSU by Jerry Boatz"

  Does it means force constant Kb, Ktheta and Kphi can be obtained from
internal coordinate transformation of normal modes?

  Can anyone give me some hints?

  Thanks and best wishes!


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