Hi,
What is the exact input you are giving to cpptraj? Thanks,
-Dan
On Mon, May 8, 2017 at 11:07 AM Chetna Tyagi <cheta231.gmail.com> 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
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon May 08 2017 - 08:30:03 PDT
