.... if :2175 :2191 :2187 :2185 :2178 :2177 are sugar ring atom number
then replace semicolon by . and it should work. semicolon (:) selects whole
residue with that residue number and @ will select that atom number
On Tue, Feb 19, 2019 at 6:04 PM mish <smncbr.gmail.com> wrote:
>
>
> 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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>> >> > >> http://lists.ambermd.org/mailman/listinfo/amber
>> >> > >>
>> >> > >>
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>> >> >
>> >> >
>> >> >
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Received on Tue Feb 19 2019 - 10:30:03 PST
