Hi,
If you want theta as well you should specify the 'theta' keyword. I
should probably make that the default for 6 member pucker calcs.
-Dan
On Tue, Feb 19, 2019 at 11:25 AM MYRIAN TORRES RICO
<myriam.torres.iiq.csic.es> wrote:
>
> Hi Mish,
>
> Thanx for your answer.
> My script is this:
>
> trajin /home/cristina/smp-196ptn/md125ns/ptn4rig_vcon.mdcrd
> pucker p1 :2175 :2191 :2187 :2185 :2178 :2177 out pucker.dat cremer
> amplitude theta range360
>
> and I obtain one only measure (phi maybe)...
>
>
> #Frame p1
> 1 2431.7465
> 2 2413.8681
> 3 2491.5866
> 4 2580.4869
> 5 2335.1242
> 6 2714.6331
> .
> .
> .
>
> why?
>
> thanx in advantage
>
> Myriam
>
>
> mish <smncbr.gmail.com> escribió:
>
> > 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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
>
>
> _______________________________________________
> 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 Tue Feb 19 2019 - 09:00:04 PST
