You need to change
:1.C1' :1.C2' :1.C3' :1.C4' :1.C5' :1.O5'
To the exact residue number (behind : ) with exact atom name (behind @ )
for your specific residue. As you can see in
0: [pucker p1 :1.C1' :1.C2' :1.C3' :1.C4' :1.C5' :1.O5' out
pucker.dat cremer amplitude theta range360]
:1.C1' (0 atoms)
:1.C2' (0 atoms)
:1.C3' (0 atoms)
:1.C4' (0 atoms)
:1.C5' (0 atoms)
Cpptraj can't find these particular atoms.
Op di 19 feb. 2019 18:47 schreef MYRIAN TORRES RICO <
myriam.torres.iiq.csic.es:
> When I use:
>
> pucker p1 :1.C1' :1.C2' :1.C3' :1.C4' :1.C5' :1.O5' out pucker.dat
> cremer amplitude theta range360
>
> The cpptraj doesn't create file.out:
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> PARM [smp-196ptnazucar.top]: Setting up 1 actions.
> 0: [pucker p1 :1.C1' :1.C2' :1.C3' :1.C4' :1.C5' :1.O5' out
> pucker.dat cremer amplitude theta range360]
> :1.C1' (0 atoms)
> :1.C2' (0 atoms)
> :1.C3' (0 atoms)
> :1.C4' (0 atoms)
> :1.C5' (0 atoms)
> Warning: Pucker::setup: One or more masks have no atoms.
> Warning: Setup failed for [pucker p1 :1.C1' :1.C2' :1.C3' :1.C4'
> :1.C5' :1.O5' out pucker.dat cremer amplitude theta range360]: Skipping
> ----- [ptn4rig_vcon3.mdcrd] (1-21, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 21 frames and processed 21 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> There is 1 data set: p1
> DATAFILE OUTPUT:
> pucker.dat: p1
> Warning: DataFile pucker.dat: Set p1 contains no data - skipping.
> Warning: DataFile pucker.dat has no sets containing data - skipping.
>
>
> --------------------------------------------------------------------------------
> I has probed this script:
>
> pucker p1 :2175 :2191 :2187 :2185 :2178 :2177 out pucker1.dat cremer
> range360
> pucker p2 :2175 :2191 :2187 :2185 :2178 :2177 out pucker2.dat
> amplitude range360
> pucker p3 :2175 :2191 :2187 :2185 :2178 :2177 out pucker3.dat theta
> range360
>
> And it has been created 3 files with differents measures (but why are
> there 3 atoms?):
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> PARM [smp-196ptnazucar.top]: Setting up 3 actions.
> 0: [pucker p1 :2175 :2191 :2187 :2185 :2178 :2177 out pucker1.dat
> cremer range360]
> :2175 (3 atoms)
> :2191 (3 atoms)
> :2187 (3 atoms)
> :2185 (3 atoms)
> :2178 (3 atoms)
> 1: [pucker p2 :2175 :2191 :2187 :2185 :2178 :2177 out pucker2.dat
> amplitude range360]
> :2175 (3 atoms)
> :2191 (3 atoms)
> :2187 (3 atoms)
> :2185 (3 atoms)
> :2178 (3 atoms)
> 2: [pucker p3 :2175 :2191 :2187 :2185 :2178 :2177 out pucker3.dat
> theta range360]
> :2175 (3 atoms)
> :2191 (3 atoms)
> :2187 (3 atoms)
> :2185 (3 atoms)
> :2178 (3 atoms)
> ----- [ptn4rig_vcon.mdcrd] (1-5672, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 5672 frames and processed 5672 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> There are 3 data sets: p1,p2,p3
> DATAFILE OUTPUT:
> pucker1.dat: p1
> pucker2.dat: p2
> pucker3.dat: p3
>
>
> -------------------------------------------------------------------------------
> Results:
>
> #Frame p1
> 1 313.8097
> 2 312.6184
> 3 313.1537
> 4 309.9323
>
> #Frame p2
> 1 121.4743
> 2 123.0577
> 3 121.8452
> 4 122.1614
> 5 55.8690
>
> #Frame p3
> 1 31.8381
> 2 27.9908
> 3 28.9717
> 4 25.6274
> 5 120.8922
>
>
>
> Could it be correct?...
>
>
> Thanx in advantage
>
> Myriam
>
>
>
>
> mish <smncbr.gmail.com> escribió:
>
> > 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
> >> > >>
> >> > >>
> >> > >> _______________________________________________
> >> > >> 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
> >>
> > _______________________________________________
> > 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 - 10:00:06 PST
