Dear Junmei,
Thank you very much. it worked fine.
Best Regards,
Sanaa
On Fri, Dec 1, 2017 at 12:43 PM, mirzo <mirzo.jinr.ru> wrote:
> Junmei Wang писал 01.12.2017 22:30:
> > 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
> >> >> >
> >> >>
> >> >> _______________________________________________
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> >> >>
> >> >>
> >> >
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Received on Fri Dec 01 2017 - 16:00:03 PST
