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

From: Daniel Roe <>
Date: Tue, 12 Nov 2019 11:21:14 -0500


As mentioned before, you can use the 'dihedral' command. One important
thing to note is that using something like 'dihedral OCCO0 @O @C1 @C2
.O' is probably not what you want, since '.O' will select *all* atoms
named O. You probably want to restrict that to a single residue, e.g.
'dihedral OCCO :1.O ...'.

If you have lots of O-C-C-O and C-O-C-C angles, you can use the
multidihedral command and define a new dihedral type, e.g.:

multidihedral OCCO D1:O:C:C:O out Dih1.dat

and so on. This assumes all the atoms are in the same residue; if not
you'll have to add an offset argument to the dihedral definition (see
the manual for full details).

For creating a histogram of the data use either the 'hist' or the
'kde' analysis commands on the data set(s) created by


On Mon, Nov 11, 2019 at 6:21 AM 조준범 <> wrote:
> Hi all,
> 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.
> Any advice would be grateful.
> _______________________________________________
> AMBER mailing list

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Received on Tue Nov 12 2019 - 08:30:02 PST
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