Can you be more specific as to what do you mean by “destructing” the structure?
In PF6 all distances and angles should be the same. From the files you show, I don’t see dihedrals or impropers. Maybe you need to set them to keep the molecule?
—
Gustavo Seabra.
> Em 30 de nov de 2017, à(s) 21:00, Sanaa ALAbbad <salabbad79.gmail.com> escreveu:
>
> 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
Received on Fri Dec 01 2017 - 03:30:03 PST
