Dear Junmei,
Thank you very much for the help.
I tried and defined frcmod as follow, YET, no luck
remark goes here
MASS
p5 30.970 1.538
Y1 19.000 0.320
Y2 19.000 0.320
Y3 19.000 0.320
Y4 19.000 0.320
Y5 19.000 0.320
Y6 19.000 0.320
BOND
p5-Y1 260.30 1.540 #forces from Phys. Chem. Chem. Phys., 2003,5,
3481-3488
p5-Y2 260.30 1.540
p5-Y3 260.30 1.550
p5-Y4 260.30 1.540
p5-Y5 260.30 1.550
p5-Y6 260.30 1.540
ANGLE
Y1 -p5-Y2 194.10 179.75 #forces from Phys. Chem. Chem. Phys.,
2003,5, 3481-3488
Y1 -p5-Y3 194.10 90.000
Y1 -p5-Y4 194.10 90.166
Y1 -p5-Y5 194.10 90.000
Y1 -p5-Y6 194.10 90.124
Y2 -p5-Y3 194.10 89.852
Y2 -p5-Y4 194.10 89.856
Y2 -p5-Y5 194.10 89.951
Y2 -p5-Y6 194.10 90.125
Y3 -p5-Y4 194.10 90.232
Y3 -p5-Y5 194.10 89.642
Y3 -p5-Y6 194.10 179.63
Y4 -p5-Y5 194.10 179.77
Y4 -p5-Y6 194.10 90.134
Y5 -p5-Y6 194.10 89.992
DIHE
IMPROPER
NONBON
p5 2.1000 0.2000
Y1 1.7500 0.0610
Y2 1.7500 0.0610
Y3 1.7500 0.0610
Y4 1.7500 0.0610
Y5 1.7500 0.0610
Y6 1.7500 0.0610
I will try following your way, hopefully it will work.
Best,
Sanaa
On Fri, Dec 1, 2017 at 10:29 AM, Junmei Wang <junmwang.gmail.com> wrote:
> Here is my solution to discriminate the two types of f-p-f angles. See the
> attached picture,
>
> f1-p-f1, f2-p-f2 and f3-p-f3 have a reference bond angle of 180 and others
> (f1-p-f2, f1-p-f3 and f2-p-f3) have a reference bond angle of 90.
>
> You can easily add f1, f2 and f3 to $AMBERHOME/dat/antechamber/PARMCHK.DAT
> (see attahcment) to make parmchk2 work.
>
> I have also attached the prepi and frcmod files for this molecule.
>
> All the best
>
> Junmei
>
>
> On Thu, Nov 30, 2017 at 7:00 PM, Sanaa ALAbbad <salabbad79.gmail.com>
> wrote:
>
> > Dear Ambers,
> >
> > I have an issue with PF6- conformational structure. During the
> > equilibration step, the octahedral geometry destroyed to square
> pyramidal.
> > I first used the frcmod generated by AMBER
> >
> > remark goes here
> > MASS
> > p5 30.970 1.538
> > f 19.000 0.320
> >
> > BOND
> > p5-f 248.60 1.646
> >
> > ANGLE
> > f -p5-f 44.040 90.000
> >
> > DIHE
> >
> > IMPROPER
> >
> > NONBON
> > f 1.7460 0.0610
> > p5 2.0940 0.2000
> >
> > and then I included the 180 angle and use the parameters used by Phys.
> > Chem. Chem. Phys., 2003,5, 3481-3488
> > that destroyed the structure even more
> >
> > remark goes here
> > MASS
> > p5 30.970 1.538
> > f 19.000 0.320
> >
> > BOND
> > p5-f 260.30 1.646
> >
> > ANGLE
> > f -p5-f 194.100 90.000
> > f -P5-f 194.100 180.00
> >
> > DIHE
> >
> > IMPROPER
> >
> > NONBON
> > f 1.7460 0.0610
> > p5 2.0940 0.2000
> >
> > Yet no luck!!
> >
> > I tried to use PARAMFIT but it defined only one angle of 90.
> >
> > Could any one help me with this regard?
> >
> > Thanks in advance.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Fri Dec 01 2017 - 10:00:04 PST
