AMBER Archive (2008)

Subject: AMBER: aromatic bent ligand

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Mon Oct 27 2008 - 21:34:49 CDT

Hi,

I have a tricyclic aromatic ligand, which is bent like a "butterfly" through two hetero-atoms atoms (X-X line) of the central ring (see scetch below). I have a structure from MOPAC. How I can set desired angle value to maintain it over MD ? In different electronic states the planarity of the compound changes.

   (top) (side; along XX line)
      X
  /\ / \ /\ X
 | | | | / \
 | | | | / \
  \/ \ / \/ / \
      X

How to set the desired value in preparation ? Will antechamber set the right torsion values to maintain the input structure in MS?

Arturas

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