Re: AMBER: dihedral angle by Ptraj

From: Esther Brugger <>
Date: Tue, 23 Jan 2007 15:02:00 -0800 (PST)

Thanks a lot for your reply! I understand it now. But if I calculate the real dihereal angles one by one, it will be a very large input dihedral commands and output files, then do the average. Is it correct?

Thomas Cheatham III <> wrote:
> I have a basic question about dihedral angles calculation by Ptraj.

The command is meant to be as generic as possible; this makes it tedious
when measuring multiple angles but more powerful... Internally, each
"angle" is stored into an array (referenced by the name specified, i.e.
"w1_resid_1a") that can be later analyzed (for example to get summary
statistics or correlations, etc).

To simplify the input, I've started to create Perl scripts to
automagically generate input for ptraj based on residue names; when this
scripting is robust I'll include these scripts with the release.

> I want to calculate a dihedral angle in residue 1 to 5, is it correct if I use following command:
> dihedral w1_resid_1a :1-5.C77 :1-5.N6 :1-5.C66 :1-5.C68 out w1_resid1_a.dat

This will compute the dihedral rotation about the virtual bond between the
center of mass of residues 1-5 atom N6 and residues 1-5 atom C68, i.e.
virtual atom 1 will be center of mass of residues 1-5 atoms C77, atom 2
will be center of mass of residues 1-5 atom N6, etc...

> or I need to specify seperatly of these angles by doing like this:
> dihedral w1_resid_1a :1.C77 :1.N6 :1.C66 :1.C68 out w1_resid1_a.dat
> dihedral w1_resid_2a :2.C77 :2.N6 :2.C66 :2.C68 out w1_resid2_a.dat
> dihedral w1_resid_3a :3.C77 :3.N6 :3.C66 :3.C68 out w1_resid3_a.dat
> dihedral w1_resid_4a :4.C77 :4.N6 :4.C66 :4.C68 out w1_resid4_a.dat
> dihedral w1_resid_5a :5.C77 :5.N6 :5.C66 :5.C68 out w1_resid5_a.dat

If you want the real angles, you will have to use the five separate
commands, although by running ptraj this should be obvious if you read the
output produced as the program runs...

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ tec3 . (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A
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Esther B.

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Received on Wed Jan 24 2007 - 06:07:44 PST
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