Hi
I am figuring out what's wrong with a cis-azobenzene transferring into a trans-azobenzene after minimisation.
The following dihedral parameters are given after running the antechamber.
I have no idea why the pk values are given zeros for the following diherals, is it correct?
in my .frcmod file, the atom symbol are like : ca, ne, nf, ha.....
And, what those :1.C3 :1.C4 :1.N1 :1.N2 means???
And, what the cordinate (1,11,12,13) means?
dihedral pk phase pn atoms
45: 0.000 3.14 3.0 :1.C3 :1.C4 :1.N1 :1.N2 (1,11,12,13)
52: 0.000 3.14 3.0 :1.C5 :1.C4 :1.N1 :1.N2 (9,11,12,13)
54: 0.000 3.14 3.0 :1.N1 :1.N2 :1.C7 :1.C8 (12,13,14,15)
55: 0.000 3.14 3.0 :1.N1 :1.N2 :1.C7 :1.C12 (12,13,14,23)
Thanks
Lin
----- Original Message -----
From: Chih-Ying Lin <chihying.usc.edu>
Date: Saturday, April 5, 2008 6:56 am
Subject: Re: AMBER: running minimisation on cis-azobenzene
To: amber.scripps.edu
>
> Hi
> Can anyone teil me any thing wrong with my revised .frcmod file ?
> WIth the revised .frcmod file, cis-azobenzene still become trans-
> azobenzene after minimisation.
>
> BEFORE REVISED
> remark goes here
> MASS
>
> BOND
>
> ANGLE
> ca-ha-ca 0.000 0.000 ATTN, need revision
> ha-ca-ha 38.000 117.650 same as ha-c2-ha
>
> DIHE
> ca-ha-ca-ca 1 0.000 0.000 0.000 ATTN,
> need revision
> ca-ha-ca-ha 1 0.000 0.000 0.000 ATTN,
> need revision
>
> IMPROPER
> ca-ca-ca-ha 1.1 180.0 2.0 General
> improper tor
> sional 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
>
>
>
>
> REVISED
> remark goes here
> MASS
>
> BOND
>
> ANGLE
> ha-ca-ha 38.000 117.650 same as ha-c2-ha
>
> DIHE
> ca-ne-nf-ca 2 76.1904 0.000 1.0
>
>
> IMPROPER
> ca-ca-ca-ha 1.1 180.0 2.0 General
> improper tor
> sional 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
>
>
>
> ----- Original Message -----
> From: Thomas Steinbrecher <steinbrt.scripps.edu>
> Date: Monday, March 31, 2008 1:37 pm
> Subject: Re: AMBER: running minimisation on cis-azobenzene
> To: amber.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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Received on Fri Apr 18 2008 - 21:17:28 PDT
