If you are using Glycam force-filed, ring atoms are named as C1, C2, C3,
C4, C5 and O5. Following command in *cpptraj* will give you angle,
amplitude and theta:
> pucker d1 :4.C1 :4.C2 :4.C3 :4.C4 :4.C5 :4.O5 out puckering.dat cremer
amplitude theta range360
analyz$ head -4 puckering.dat
#Frame d1 d1[Amp] d1[Theta]
1 112.9888 0.5533 170.4752
2 27.2829 0.5627 164.2702
3 95.4169 0.6143 172.6282
all the best.
On Tue, Feb 19, 2019 at 1:52 PM Pratul Agarwal <pratul.agarwal-lab.org>
wrote:
> Hi Myriam,
>
> Has anyone replied to your query? I didn't see any response.
>
> Have you tried using cpptraj? The command will be:
> >pucker p1 :1.C1’ :1.C2’ :1.C3’ :1.C4’ :1.O4’ range360 out pucker.dat
>
> See the manual for further details.
>
> Pratul
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
> On 2/18/2019 12:54 PM, MYRIAN TORRES RICO wrote:
>
> Hi all,
>
> I have a complex protein-saccharide and I want to calculate the
> puckering coordinates (q,f) in the six ring. How is the scrypt?
>
> thanx in advantage
>
> Myriam
>
>
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Received on Tue Feb 19 2019 - 08:30:02 PST
