Date: Wed, 3 Oct 2018 20:27:32 +0530
Dear Amber Users
I have equilibrated the protein-water system and after 15ns when I have
generated the pdb file using ptraj, it appears that the part of the protein
(intrinsically disordered protein typically looks like a random coil) comes
out of the box.
ptraj script used for generating the pdb file is given below:
trajin pro_prod4.mdcrd
center :1-42
image center familiar
trajout pro_prod4 pdb
For visualization, I have attached the snapshot of the protein-water system.
>From Leena Aggarwal
Department of Chemistry
University of Delhi
Delhi
India
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(image/png attachment: Screenshot_from_2018-10-03_20-19-44.png)
