On Tue, Feb 19, 2019 at 4:42 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
Aren't you picking up full residues while using ":2175" syntax? To Can
you provide log from *cppctraj* to understand what is happening?
> > 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
> > >>
> > >>
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Received on Tue Feb 19 2019 - 09:00:05 PST
