[AMBER] Help with imagining curled protein

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Tue, 13 Jul 2021 09:31:03 -0400

Dear Amber Community,

My fairly straight, filamentous protein curled during dynamics, and I’m struggling to find a way to image it back into the box, if possible. I want to post-process the energetics with an implicit solvent, but I’m concerned that the results will be meaningless unless I figure out how to image the protein correctly. Because it’s a homotrimeric complex, I’ve tried the below script for imaging in cpptraj

parm xxx.parm7
reference xxx.rst7
trajin xxx.mdcrd
trajout yyy.mdcrd

center :1-282 mass origin #domain 1
image origin center
center :1-564 mass origin #domain 1-2
image origin center
center :1-846 mass origin #domain 1-3
image origin center

But I still get the below (figures attached from 2 different frames). What can/should I try? How much of this issue is a visualization problem and won’t affect a non-periodic (implicit solvent) calculation?

Best regards,

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Received on Tue Jul 13 2021 - 07:30:03 PDT
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