Thanks so much Elvis..this worked for me..
On Mon, May 8, 2017 at 6:51 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> It will be easier to change atom masks while using cpptraj than change
> atoms names in trajectories.
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Chetna Tyagi [mailto:cheta231.gmail.com]
> Sent: Monday, May 08, 2017 8:38 PM
> To: amber.ambermd.org
> Subject: [AMBER] Cpptraj calculates only three PHI-PSI angles in a
> 18-residue long peptide
>
> 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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>
--
Best wishes
Chetna
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Received on Mon May 08 2017 - 11:00:03 PDT
