AMBER Archive (2008)

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

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Mon Apr 07 2008 - 23:40:20 CDT

Hi Thomas:
How could I know that my system really has a double bond?
I have check all the force parameters and atom types.
ne (sp2)
nf (sp2)

I also set an extremely large force field parameter for ca-ne-nf-ca as 100000kcal/mole.
Unfortunately, the cis still goes to trans structures.

Thanks
Lin

----- Original Message -----
From: Thomas Steinbrecher <steinbrt_at_scripps.edu>
Date: Monday, April 7, 2008 10:50 am
Subject: Re: AMBER: running minimisation on cis-azobenzene
To: amber_at_scripps.edu

> What I meant is,
>
> check if your system really has a double bond where you expect one
> to be
> by examining the forcefield parameters and atom types set. Older
> versions
> of antechamber/gaff sometimes did not handle complex conjugated
> systems
> well (i.e. did not place a double bond where one should be). Since
> you see
> cis/trans-isomerization, my guess would be that there is no double
> bond
> set.
>
> Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
>
> On Mon, 7 Apr 2008, Chih-Ying Lin wrote:
>
> >
> >
> > 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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