On Tue, Feb 19, 2019 at 1:04 PM mish <smncbr.gmail.com> wrote:
> 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:
Note: you can also check this from inside cpptraj without writing a
PDB. Try the 'atoms' command, e.g.
```
> parm tz2.parm7
[parm tz2.parm7]
Reading 'tz2.parm7' as Amber Topology
> atoms :1
[atoms :1]
#Atom Name #Res Name #Mol Type Charge Mass GBradius El rVDW eVDW
1 N 1 SER 1 N3 0.1849 14.0100 1.5500 N 1.8240 0.1700
2 H1 1 SER 1 H 0.1898 1.0080 1.2000 H 0.6000 0.0157
3 H2 1 SER 1 H 0.1898 1.0080 1.2000 H 0.6000 0.0157
```
-Dan
PS - Parmed has similar functionality; the command is "printDetails" I think.
> 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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Received on Tue Feb 19 2019 - 11:00:03 PST
