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 - 11:30:02 PST
