AMBER Archive (2008)

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

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Tue Apr 08 2008 - 17:00:20 CDT

Hi Junmei Wang:
what do you mean the V1 term and the V2 term of the ca-ne-nf-ca?

Thanks
Lin

----- Original Message -----
From: Junmei Wang <junmwang_at_gmail.com>
Date: Tuesday, April 8, 2008 2:42 pm
Subject: Re: AMBER: running minimisation on cis-azobenzene
To: amber_at_scripps.edu

> Hi, the cis-conformation is much less favorable than the trans.
> Most force
> fields including mmff and gaff produce the trans conformation after
> theminimization (starting from a cis conformation). But you can get
> the cis
> conformation by either using restraint or modifying the force field
> parameters. For this particular molecule, you may delete the V2
> term of
> ca-ne-nf-ca and change the phase angle of V1 term from 0 to 180.0.
> Afterthis modification, I can get the cis conformation. Here are
> some tips: using
> the latest parmchk in ambertools to produce all the force field
> parametersfor the molecule (using -a Y flag), and manually modify
> the involved
> torsional angle parameters. But I prefer to use restraint, rather
> than to
> modify the force field parameters.
>
> By the way, it seems to me there is a problem with your prepi or
> mol2 file
> since there should no missing bond angle parameters.
>
> Best
>
> Junmei
>
>
> On Mon, Apr 7, 2008 at 11:40 PM, Chih-Ying Lin <chihying_at_usc.edu>
> wrote:
> >
> >
> > 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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