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
>> >> >
>> >>
>> >> _______________________________________________
>> >> 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
>>
> _______________________________________________
> 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
Received on Fri Dec 01 2017 - 12:00:05 PST
