AMBER: dihedral angle by Ptraj

From: Esther Brugger <>
Date: Tue, 23 Jan 2007 10:24:42 -0800 (PST)

Dear All,
 I have a basic question about dihedral angles calculation by Ptraj.
 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
 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
 I am just wondering if I use ":1-5" command, the program will calculate the angles between the residues, for example:
 :1.C77 :2.N6 :2.C66 :2.C68
 Any help will be grealtly appreciated.

Esther B.

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Received on Wed Jan 24 2007 - 06:07:41 PST
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