Dear Amber User,
I have run 50ns simulation of an intrinsically disordered protein. The protein's C-terminal region is very flexible and when I visualize the mdcrd of the trajectories two to three residues of the protein comes out of the water box. I use the under mention commands to re-image the mdcrd trajectories but still the protein comes out of the water box. Actually it comes out and goes back again than flexes out again. Is this is going to affect my analysis if yes how to correct it.
trajin apo_prod4.mdcrd
center :1-247 mass origin
image origin center familiar
trajout reimaged_prod4.mdcrd
Dr Nida Baig
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Received on Fri Jul 22 2016 - 04:30:02 PDT
