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

From: Elvis Martis <elvis_bcp.elvismartis.in>
Date: Tue, 12 Nov 2019 15:30:53 +0530

For probability distribution either import the
Data you obtain on to an excel sheet and the histograms.
Or else use hist command in cpptraj for the same.
Look up in the amber manual for hist command to know how to use it.

I hope that helps
On Tuesday, November 12, 2019, 조준범 <j1300704.gmail.com> wrote:

> 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
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Best Regards
> > Elvis Martis
> > Mumbai.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>

```--
Best Regards
Elvis Martis
Mumbai.
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Received on Tue Nov 12 2019 - 02:30:02 PST
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