Dear Amber users,
upon analysing a PBC simulation with a ligand non-covalently interacting
with a protein, I observed large jumps of tenth of angstroms when
plotting the distances between the center of masses of the protein and
the ligand. I attributed this to jumps caused by periodic boundary
conditions, placing e.g. the ligand in a different imaginary box than
the protein. Extracting one snap out of the trajectory clearly shows
that the ligand is located side-by-side to the protein, separated by
more than 40 angstrom.
Trying to image the ligand back into the box with the protein (using
ptraj by centering to the protein and imaging only the ligand) resulted
in a complex where the ligand clashes into the protein structure.
My question is:
Is this the correct way to re-generate a "normal" protein-ligand complex
within the same box e.g. to visualize the interactions? Is there
something wrong with my considerations or can you recommend me a
procedure to make "real" complexes for visualisation.
Thanks a lot for any advice!
Best wishes,
-Harald
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Received on Fri Jun 29 2012 - 08:00:03 PDT
