AMBER Archive (2008)

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

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Apr 08 2008 - 17:11:35 CDT

Hi,
There is no problem with the prep file.

The following is the orginal gaff force field parameters for this molecule

remark goes here
MASS
ca 12.010 0.360
ha 1.008 0.135
ne 14.010 0.530
nf 14.010 0.530

BOND
ca-ha 344.30 1.087
ca-ca 478.40 1.387
ca-ne 361.80 1.431
ne-nf 738.60 1.257
nf-ca 361.80 1.431

ANGLE
ca-ca-ha 48.500 120.010
ca-ca-ca 67.200 119.970
ca-ca-ne 67.700 119.880
ca-ne-nf 69.900 114.720
ne-nf-ca 69.900 114.720
nf-ca-ca 67.700 119.880

DIHE
ca-ca-ca-ha 1 3.625 180.000 2.000
ca-ca-ca-ca 1 3.625 180.000 2.000
ca-ca-ne-nf 1 0.000 180.000 3.000
ha-ca-ca-ha 1 3.625 180.000 2.000
ha-ca-ca-ne 1 3.625 180.000 2.000
ca-ca-ca-ne 1 3.625 180.000 2.000
ca-ne-nf-ca 1 3.000 180.000 -2.000
ca-ne-nf-ca 1 2.800 0.000 1.000
ne-nf-ca-ca 1 0.000 180.000 3.000
nf-ca-ca-ha 1 3.625 180.000 2.000
nf-ca-ca-ca 1 3.625 180.000 2.000

IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
ca-ca-ca-ne 1.1 180.0 2.0 Using default
value
ca-ca-ca-nf 1.1 180.0 2.0 Using default
value

NONBON
  ca 1.9080 0.0860
  ha 1.4590 0.0150
  ne 1.8240 0.1700
  nf 1.8240 0.1700

After modified the line "ca-ne-nf-ca 1 2.800 0.000
1.000"
to "ca-ne-nf-ca 1 2.800 180.000 1.000". I could get
the cis conformation.

Junmei

>
>
> ----- 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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