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

From: Chetna Tyagi <cheta231.gmail.com>
Date: Mon, 8 May 2017 17:07:34 +0200

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

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

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Received on Mon May 08 2017 - 08:30:02 PDT
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