AMBER Archive (2006)

Subject: AMBER: PTRAJ generating wrong dihedral angles

From: hayden (
Date: Tue Jan 10 2006 - 05:40:05 CST

Dear Amber users

I have been using PTRAJ to extract dihedral angles for a system using amber
generated pdb files and the corresponding prmtop file.

However, on comparing the ptraj calculated dihedral angles to those obtained
from VMD I noticed substantial differences. Indeed, it appears that the
ptraj derived dihedrals are wildly wrong.

The input file I used for ptraj was named

trajin ptraj.coords #file ptraj.coords is an "ambpdb" generated pdb file
#residue 11
dihedral phi_11 :11_at_C :12_at_N :12_at_CA :12_at_C out __phi_11
dihedral psi_11 :11_at_N :11_at_CA :11_at_C :12_at_N out __psi_11
#residue 12
dihedral phi_12 :12_at_C :13_at_N :13_at_CA :13_at_C out __phi_12
dihedral psi_12 :12_at_N :12_at_CA :12_at_C :13_at_N out __psi_12
#residue 13
dihedral phi_13 :13_at_C :14_at_N :14_at_CA :14_at_C out __phi_13
dihedral psi_13 :13_at_N :13_at_CA :13_at_C :14_at_N out __psi_13


The above input was generated using a format akin to that specified in the
amber “PTRAJ tutorial” site:

To run the script I used: --> ptraj

The above procedure produced dihedrals that are wrong. Considering just the
phi angles I got:

Residue 11: 125.0
Residue 12:-168.6
Residue 13: 89.9

for the input lines shown in "" above.

I know they are wrong because I tested a structure that was already known to
have beta sheets, and the PTRAJ calculated torsion angles fell way outside
the range of allowed Ramachandran values. The values according to vmd are:

Residue 11: -129.8
Residue 12: -114.9
Residue 13: -93.7

which I presume are right since they fall into allowed Ramachandran phi

Has anyone else suffered problems of this nature, or is there something that
I've missed?

Many thanks in advance

Hayden Eastwood
Perdita Barran Research Group
Joseph Black Building
Edinburgh University
West Mains Road
Tel: 0131 650 4773
Research page:
"You have to be an academic to believe some things; no ordinary person would
be so stupid." -George Orwell

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