AMBER Archive (2008)

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

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Apr 08 2008 - 16:37:54 CDT

Hi, the cis-conformation is much less favorable than the trans. Most force
fields including mmff and gaff produce the trans conformation after the
minimization (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. After
this modification, I can get the cis conformation. Here are some tips: using
the latest parmchk in ambertools to produce all the force field parameters
for 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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