Re: [AMBER] PF6- octahedral geometry change during equilibration!!

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Fri, 1 Dec 2017 08:23:40 -0300

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.
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Received on Fri Dec 01 2017 - 03:30:03 PST
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