AMBER: Dihedral analysis

From: Claire Zerafa <>
Date: Mon, 03 Jul 2006 21:25:33 +0000

Dear amber users

I am trying to do some dihedral analysis.

I use rdparm and call my parmtop file, and then look at the dihedral
angles of interest by using printdihedral :.36 to look at the dihedral
bonds in amino acid 36- in this case leucine. My result is as follows:

RDPARM MENU: printdihedral :.36
Mask [:.36] represents 1 atoms

Dihedral pk phase pn atoms
      70: 0.150 0.00 3.0 :3.HG3 :3.CG :3.CB :3.HB2
      71: 0.150 0.00 3.0 :3.HG3 :3.CG :3.CB :3.HB3
      72: 0.160 0.00 3.0 :3.HG3 :3.CG :3.CB :3.CA
      79: 0.156 0.00 3.0 :3.HD3 :3.CD :3.CG :3.HG3
      83: 0.156 0.00 3.0 :3.HD2 :3.CD :3.CG :3.HG3
      89: 0.156 0.00 3.0 :3.N :3.CD :3.CG :3.HG3

My questions are as follows:

1. The number of dihedral atoms found is different to the preceding
leucine I was looking at:

RDPARM MENU: printdihedrals :.33
Mask [:.33] represents 1 atoms

Dihedral pk phase pn atoms
      24: 0.000 0.00 2.0 :2.C :3.N :3.CD :3.HD3
      77: 0.000 0.00 2.0 :3.HD3 :3.CD :3.N :3.CA
      78: 0.156 0.00 3.0 :3.HD3 :3.CD :3.CG :3.HG2
      79: 0.156 0.00 3.0 :3.HD3 :3.CD :3.CG :3.HG3
      80: 0.156 0.00 3.0 :3.HD3 :3.CD :3.CG :3.CB

I guess this is due to the way in which leucin is bound to adjacent
amino acids in the protein??

2. I would like, from this output, to identify how the phi psi chi and
omega angles vary with time, over the courseof my trajectory. If I
consider phi angles for example then I would look for a N-CA linkage,
which exists in aa 33:

77: 0.000 0.00 2.0 :3.HD3 :3.CD :3.N :3.CA (33,31,30,40)

but not for aa 36 (both leucines). But logically, this dihedral angle
must exist in both amino acids... Can someone explain this please?

3. Another thing I notice is that apparently, the dihedral angle entries
for the specific amino acids I request are not restricted to the amino
acid of interest, but also dihedral bonds made with adjacent residues
are included ( Iassume this is what the four nubers within the brackets
mean?) Is there a way to restrict output to the amino acid of interest only?

4. My final issue is nomenclature for use in ptraj. My intention is to
run dihedral time series in ptraj. The output from rdparm above uses 3.
and 2. irrespective of the aa beind considered. How do I refer to the
specific atom in ptraj based on my rdparm output?

I am doing this for the first time, and I am sorry if my questions seem

Thanks in advance


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 05 2006 - 06:07:14 PDT
Custom Search