Dear Amber users,
I have performed MD simulations on a trimeric protein complex (let's say
protein A, B and C). I have run the simulations using the iwrap=1 option.
At a certain point of the dynamics, part of the C protein "got out of the
box", and now I'm having trouble imaging the resulting trajectories using
cpptraj. I've tried centering in a sequential way, first protein A, then
A-B, then A-B-C (that worked for me in the past) without good results. I've
also followed without success Dan Roe suggestions posted in
http://archive.ambermd.org/201207/0443.html.
Have you ever had this type of problem? Any suggestion would be appreciated
Thanks
Ari
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Received on Fri Oct 02 2020 - 07:30:02 PDT
