# Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ

From: 조준범 <j1300704.gmail.com>
Date: Tue, 12 Nov 2019 17:16:39 +0900

Thanks for advice. I get some numbers.

But, do I have to index it manually?
What I want is probability distribution of O-C-C-O and C-O-C-C angles.
Such as the figure below.

[image: image.png]

2019년 11월 12일 (화) 오후 12:33, Elvis Martis <elvis_bcp.elvismartis.in>님이 작성:

> Hello
> Try this and also mention the residue number after :
> :<residue number>.<Atom name>
> dihedral OCCO0 :.O :.C1 :.C2 :.O out dihedral.dat (it shows 0)
> dihedral OCCO1 :.O :.C1 :.C1 :.O out dihedral.dat (it shows nan)
> dihedral OCCO2 :.O :.C2 :.C2 :.O out dihedral.dat (it shows nan)
> dihedral OCCO3 :.O ":.CT|.C1|.C2" ":.CT|.C1|.C2" :.O out dihedral.dat (it
> shows
> nan)
>
> On Tuesday, November 12, 2019, 조준범 <j1300704.gmail.com> wrote:
>
> > Thank you for advice.
> >
> > I've tried but results show all zeros or nans. Why it happens?
> > My commands are as follow.
> >
> > dihedral OCCO0 .O .C1 .C2 .O out dihedral.dat (it shows 0)
> > dihedral OCCO1 .O .C1 .C1 .O out dihedral.dat (it shows nan)
> > dihedral OCCO2 .O .C2 .C2 .O out dihedral.dat (it shows nan)
> > dihedral OCCO3 .O ".CT|.C1|.C2" ".CT|.C1|.C2" .O out dihedral.dat (it
> shows
> > nan)
> >
> > 2019년 11월 11일 (월) 오후 9:50, David A Case <david.case.rutgers.edu>님이 작성:
> >
> > > On Mon, Nov 11, 2019, 조준범 wrote:
> > > >
> > > >I have no idea about how to calculate dihedral distribution.
> > > >What command should I use? 'dihedral' or 'multidihedral' or
> > > >'clusterdihedral'?
> > > >
> > > >I want to see the distribution of O-C-C-O and C-O-C-C of PEO.
> > >
> > > The 'dihedral' command is what you want here; you would issue two such
> > > commands, one for each of the two dihedrals you want.
> > >
> > > ....good luck....dac
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> >
> > *Junbeom Cho*
> >
> > Integrated Ph. D. Student
> >
> >
> >
> > Theoretical and Computational Soft Matters Laboratory
> >
> > School of Chemical and Biological Engineering
> >
> > Seoul National University
> >
> > 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
> >
> >
> >
> > Tel: +82-2-880-1529
> >
> > E-mail: cjb0704.snu.ac.kr
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Best Regards
> Elvis Martis
> Mumbai.
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(image/png attachment: image.png)

Received on Tue Nov 12 2019 - 00:30:02 PST
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