Hi Sanaa,
Here is my tleap
source leaprc.gaff
loadamberprep PF6.prepi
loadamberparams PF6.frcmod
saveamberparm PF6 PF6.prmtop PF6.prmcrd
quit
The PF6.mol2 I sent to you has sybyl atom types. You need to run
antechamber to get a pdf file
antechamber -fi mol2 -fo pdb -i PF6.mol2 -o PF6.pdb -rn PF6.
You may use this PF6.pdb to generate topology.
source leaprc.gaff
loadamberparams PF6.frcmod
loadamberprep PF6.prepi
mol=loadpdb PF6.pdb
saveamberparm mol PF6.prmtop PF6.prmcrd
quit
Let me know if this procedure works for you or not.
All the best
Junmei
On Fri, Dec 1, 2017 at 2:13 PM, Sanaa ALAbbad <salabbad79.gmail.com> wrote:
> Dear Junmei,
>
> I noticed the error in the prmtop file is not defining more than one bond
> or angle values! although it is listed in the frcmod file.
> But in the prmtop file you sent me it has listed all bond and angles.
>
> This how I generated prmtop:
> >tleap
> >source leaprc.gaff
> >loadamberparams PF6.frcmod
> >PF6=loadmol2 PF6.mol2
> >saveoff PF6 PF6.lib
> >saveamberparm PF6 PF6.prmtop PF6.inpcrd
>
> any idea
> Thanks,
> Sanaa
>
> On Fri, Dec 1, 2017 at 10:41 AM, Sanaa ALAbbad <salabbad79.gmail.com>
> wrote:
>
> > 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/PAR
> >> MCHK.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
> >> >
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
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Received on Fri Dec 01 2017 - 12:00:03 PST
