AMBER Archive (2008)

Subject: AMBER: Collect dihedral angles

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Wed Apr 09 2008 - 16:35:09 CDT

 Hi
 to collect the dihedral angles

after the command
 
 $AMBERHOME/exe/ptraj azocisbenzene.prmtop <measure_trp_angles.ptraj.txt > cis_dihedral.out
 
 I could not get the azocisbenzene_phi.dat...... or cis_dihedral.out.....
 
the file : measure_trp_angles.ptraj.txt
trajin azocisbenzene_vac_md1_12Acut.mdcrd
dihedral trpphi :1_at_C4 :1_at_N1 :1_at_N2 :1_at_C7 out azocisbenzene_phi.dat

 where 1_at_C4, 1_at_N1, 1_at_N2 and 1_at_C7 are defined in the prmtop file

 thanks
 Lin

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