AMBER Archive (2008)

Subject: Re: AMBER: running minimisation on cis-azobenzene

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Mon Apr 07 2008 - 12:31:51 CDT

Hi Thomas:
 (alternatingsingle-double bonds used to confuse older versions of
 antechamber, Im not sure that is still a danger...)

What do you mean by this ?

Thanks
Lin

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