AMBER Archive (2009)

Subject: Re: [AMBER] question with pucker in six member ring

From: Nicolas Sapay (nicolas.sapay_at_cermav.cnrs.fr)
Date: Fri Oct 16 2009 - 10:04:24 CDT

Ganesh Kamath a écrit :
> Hi all,
>
Hi Ganesh,

I can only advise you to read some litterature about the Cremer-Pople
ring puckering. This paper may also interest you:

    Haasnoot, The conformation of six-membered rings described by
    puckering coordinates derived from endocyclic torsion angles, J Am
    Chem Soc, 1992, 114, 882-887

Cheers,
Nicolas

> I am trying to calculate the pucker in a six member ring. I use this lines
> in ptraj
>
> trajin data-0.00.crd
> pucker name1 :233_at_C6 :233_at_C7 :233_at_N8 :233_at_C8A :233_at_C4A :233_at_N5 out
> puckerDHPpseudo.dat cremer offset -90.0
> pucker name2 :233_at_C6 :233_at_C7 :233_at_N8 :233_at_C8A :233_at_C4A :233_at_N5 out
> puckerDHPamp.dat cremer amplitude offset -90.0
> go
>
>
> For the amplitude I get the output
>
> 1.00 90.048991
> 2.00 90.045684
> 3.00 90.033221
> 4.00 90.094447
> 5.00 90.075243
> 6.00 90.126185
> 7.00 90.107877
> 8.00 90.065907
> 9.00 90.095487
> 10.00 90.103874
>
>
> and for pseudorotate
>
> 1.00 95.892046
> 2.00 70.439829
> 3.00 -150.576896
> 4.00 171.025833
> 5.00 165.689818
> 6.00 152.105514
> 7.00 142.713603
> 8.00 -164.182655
> 9.00 148.811860
> 10.00 150.728189
> 11.00 140.514928
> 12.00 5.599644
>
> Could some please help me understand this. thanks, ganesh
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