Hi :
Here is cis-azobenzene prepi file and I don;t have the mol2 file.
Honestly, I don't know how to read the prepi file.
0 0 2
This is a remark line
molecule.res
MOL INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C3 ca M 3 2 1 1.540 111.208 180.000 -0.12270
5 H3 ha E 4 3 2 1.140 119.532 0.578 0.14186
6 C2 ca M 4 3 2 1.540 5.613 -95.332 -0.12886
7 H2 ha E 6 4 3 1.140 120.036 87.001 0.13651
8 C1 ca M 6 4 3 1.539 119.993 -92.985 -0.11813
9 H1 ha E 8 6 4 1.140 120.035 179.710 0.13521
10 C6 ca M 8 6 4 1.540 119.957 -0.389 -0.13449
11 H5 ha E 10 8 6 1.140 120.015 -179.224 0.13693
12 C5 ca M 10 8 6 1.540 120.032 1.168 -0.08903
13 H4 ha E 12 10 8 1.140 119.988 179.503 0.14793
14 C4 ca M 12 10 8 1.539 120.042 -0.091 0.03092
15 N1 ne M 14 12 10 1.512 119.668 178.559 -0.13606
16 N2 nf M 15 14 12 1.482 121.078 -172.263 -0.13612
17 C7 ca M 16 15 14 1.512 121.005 5.981 0.03101
18 C8 ca M 17 16 15 1.540 119.752 -170.324 -0.08918
19 H6 ha E 18 17 16 1.140 119.977 -1.074 0.14789
20 C9 ca M 18 17 16 1.540 119.978 178.889 -0.13442
21 H7 ha E 20 18 17 1.140 119.978 -179.665 0.13692
22 C10 ca M 20 18 17 1.540 120.044 0.478 -0.11820
23 H8 ha E 22 20 18 1.140 119.972 -179.357 0.13520
24 C11 ca M 22 20 18 1.540 119.970 1.251 -0.12881
25 H9 ha E 24 22 20 1.139 120.026 179.149 0.13649
26 C12 ca M 24 22 20 1.540 119.981 -0.691 -0.12272
27 H10 ha E 26 24 22 1.140 119.992 179.054 0.14185
LOOP
C4 C3
C12 C7
IMPROPER
C4 C2 C3 H3
C3 C1 C2 H2
C2 C6 C1 H1
C5 C1 C6 H5
C4 C6 C5 H4
C5 C3 C4 N1
C8 C12 C7 N2
C7 C9 C8 H6
C8 C10 C9 H7
C9 C11 C10 H8
C10 C12 C11 H9
C7 C11 C12 H10
DONE
STOP
----- Original Message -----
From: Junmei Wang <junmwang.gmail.com>
Date: Tuesday, April 8, 2008 2:42 pm
Subject: Re: AMBER: running minimisation on cis-azobenzene
To: amber.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.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.scripps.edu>
> > Date: Monday, April 7, 2008 10:50 am
> > Subject: Re: AMBER: running minimisation on cis-azobenzene
> > To: amber.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.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 - 21:18:00 PDT
