Looking through the documentation several times and spending several hours on various ideas, I decided that I needed a hand. I am writing Python software that goes through NAMD modeling of RADA proteins, calculating the various values that interest us.
Currently, my code goes through every time step, then goes through every atom in the system, performing various analytical steps.
What I need to do is to combine each amino acid into my own "atom" (a one-position representation of the amino acid located in the center of the mass residues).
Is it possible to create new atoms and add them to the MDAnalysis Universe? Can I populate these new atoms with data such as my amino acid center, human-readable name, etc.
Sort of:
u = MDAnalysis.Universe(psf, coordDcd) ag = u.selectAtoms(" the atoms in my amino acid ") amino_acid = MDAnalysis.Atom amino_acid.pos = ag.centerOfMass()
I know how to read the NAMD simulation (.dcd files), and all atoms are represented by a fine, but in the end I need to turn ~ 20 atoms into one “averaged” atom (to simplify the calculations).
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