AMBER Archive (2008)

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

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Tue Apr 08 2008 - 17:27:52 CDT

Hi
Where do you get the original gaff force field parameter ?
I am using Amber9, I only get the .prmtop file and frcmod file after running antechamber.

The phase angle for ca-ne-nf-ca is 0.0 , which is written in one paper.
And, for the GROMOS 96,
V(phi)=K0/2(1-cos2*phi), K0=84kJ/mol.

After setting phase angle=180, I also get cis-structure after minimisation.

Thanks
Lin

----- Original Message -----
From: Junmei Wang <junmwang_at_gmail.com>
Date: Tuesday, April 8, 2008 3:15 pm
Subject: Re: AMBER: running minimisation on cis-azobenzene
To: amber_at_scripps.edu

> 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
> impropertorsional angle (2 general atom types)
> ca-ca-ca-ne 1.1 180.0 2.0 Using
> defaultvalue
> ca-ca-ca-nf 1.1 180.0 2.0 Using
> defaultvalue
>
> 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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