AMBER Archive (2007)

Subject: AMBER: dihedral angle by Ptraj

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Tue Jan 23 2007 - 12:24:42 CST

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_at_C77 :1-5_at_N6 :1-5_at_C66 :1-5_at_C68 out w1_resid1_a.dat
 
 or I need to specify seperatly of these angles by doing like this:
 
 dihedral w1_resid_1a :1_at_C77 :1_at_N6 :1_at_C66 :1_at_C68 out w1_resid1_a.dat
 dihedral w1_resid_2a :2_at_C77 :2_at_N6 :2_at_C66 :2_at_C68 out w1_resid2_a.dat
 dihedral w1_resid_3a :3_at_C77 :3_at_N6 :3_at_C66 :3_at_C68 out w1_resid3_a.dat
 dihedral w1_resid_4a :4_at_C77 :4_at_N6 :4_at_C66 :4_at_C68 out w1_resid4_a.dat
 dihedral w1_resid_5a :5_at_C77 :5_at_N6 :5_at_C66 :5_at_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_at_C77 :2_at_N6 :2_at_C66 :2_at_C68
 
 Any help will be grealtly appreciated.
 
 

Esther B.

 
---------------------------------
Don't get soaked. Take a quick peak at the forecast
 with theYahoo! Search weather shortcut.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu