Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide

From: Daniel Roe <>
Date: Mon, 08 May 2017 15:14:26 +0000


What is the exact input you are giving to cpptraj? Thanks,


On Mon, May 8, 2017 at 11:07 AM Chetna Tyagi <> wrote:

> Dear all,
> I have a peptide with few non-standard amino acid residues which I made
> using RED server and carried out this 100 ns long simulation. All other
> analysis like time-evolution of Hydrogen bonds and RMSD is calculated
> without errors. But while calculating phi-psi angles as a function of time
> it only calculates for three residues each. These 3 residues are the
> standard ones.
> Phi-4, Phi-5, Phi-15 and Psi-3, Psi-4, Psi-14
> The error for other angle calculation is "one or more atom masks have no
> atoms"
> I believe it can be due to a different atom numbering convention being
> used, like CA is C1 and C is C6 or C7 etc. The same happens when I compute
> these angles using the Python MDtraj online module. How can I change this
> in a trajectory? Is it possible?
> Thanks in advance
> --
> Best wishes
> Chetna
> _______________________________________________
> AMBER mailing list
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
AMBER mailing list
Received on Mon May 08 2017 - 08:30:03 PDT
Custom Search