AMBER: Minimisation: cis-azobenzene parameters

From: Chih-Ying Lin <chihying.usc.edu>
Date: Sat, 05 Apr 2008 06:45:34 -0700

Hi
I wanna know which file records the complete force field parameters for the compound -cisazobenzene which is dealt
with the antechamber.

thanks
Lin




----- Original Message -----
From: Thomas Steinbrecher <steinbrt.scripps.edu>
Date: Monday, March 31, 2008 1:37 pm
Subject: Re: AMBER: running minimisation on cis-azobenzene
To: amber.scripps.edu

> Hi Lin,
>
> cis-transisomerization of a double bond cannot occur in a
> minimization. Is
> your starting conformation really a cis-azobenzene? Does it have
> huge
> clashes that might disrupt your structure? Unless you have very
> strange
> parameters set, what you see will indeed not occur during a
> minimization
> unless things go very wrong.
>
> Check the atom types antechamber has set for your molecule and look
> up the
> dihedrals that apply if you really have a double bond there
> (alternatingsingle-double bonds used to confuse older versions of
> antechamber, Im not
> sure that is still a danger...)
>
> Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
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Received on Fri Apr 18 2008 - 21:17:03 PDT
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