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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Received on Mon May 08 2017 - 10:00:02 PDT
