On Tue, Feb 19, 2019 at 5:47 PM MYRIAN TORRES RICO <
myriam.torres.iiq.csic.es> wrote:
> When I use:
>
> pucker p1 :1.C1' :1.C2' :1.C3' :1.C4' :1.C5' :1.O5' out pucker.dat
>
Write a pdb file on cpptraj (or if you have one from tleap) and check
residue number of your monosaccharide. If you used glycam then try:
pucker d1 :n.C1 :n.C2 :n.C3 :n.C4 :n.C5 :n.O5 out puckering.dat cremer
amplitude theta range360
replace n by the exact residue number of monosaccharide in your pdb file.
If you used gaff of something else, look at the pdb file and also replace
C1, C2, C3, C4, C5, O5 by the respective sugar ring atom names. do not use
quotes unless you have them in your atom names.
> 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?):
>
It is likely that :2175 :2191 :2187 :2185 :2178 :2177 are water residues
and you are picking up them. Look at the page 395 of Amber18 manual (19.1
Amber Masks) for better understanding of selecting 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
> >> > >>
> >> > >>
> >> > >> _______________________________________________
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> >> > >>
> >> > >>
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> >> >
> >> >
> >> >
> >> >
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> >>
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>
>
>
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Received on Tue Feb 19 2019 - 10:30:02 PST
