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
Received on Tue Feb 19 2019 - 10:00:05 PST
