Hi AMBERists,
I am having issues in reimaging the MD simulations of a Protein in an orthorombic box of water. I want to check the permeability of the catalytic pocket through the homodimeric structure of the protein, if a different number of water molecules get into the active site of each monomer. To do this I thought to calculate the coordination number of the metal centre in the active site vs. water molecules. You might suggest a different strategy for doing this - am open to suggestions, of course.
My issue comes from the attempts of reimaging the trajectories as I thought water molecules should be included to measure how many of those get into the different pockets. The output coming from my cpptraj script seems to have the water box centred but not the protein, the protein always looks shifted from the centre of the box and there are "cavities" in the water box. My script looks like this:
parm Protein.prmtop
trajin Protein_md10ns.mdcrd 0 last 50
unwrap :1-1640 #the protein is 1640 amino acid long
image origin center :1-1640 familiar
center :1-1640 mass origin
autoimage
trajout Reimaged_trajectories.nc netcdf
Kind regards,
Damiano
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Received on Mon Nov 28 2022 - 03:30:02 PST
