AMBER Archive (2009)

Subject: [AMBER] aromatic ring getting distorted

From: Jio M (jiomm_at_yahoo.com)
Date: Fri Dec 04 2009 - 04:03:49 CST

Dear Amber users;

I have a ring system like shown in two attached files which is to be
used as ligands.When I run dynamics the ring system get distorted more
or less like cyclohexane ring. This should NOT happen according to atom
types.

I tried by changing atom type cc (cc.png attached) to cp (cp.png
attached) so that they correspond to carbon atoms attaching two rings.
But when I run dynamics (imin=0) Amber is considering rings to be
cyclohexane like not aromatic though I have not changed the atom types
of other atoms.

Should I define bond-order by myself and also should I change atom type from cc to cp?

thanks and regards;

JIomm

      

  • image/png attachment: cc.png

  • image/png attachment: cp.png

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