[AMBER] Part of protein going out of the box

From: Leena Aggarwal <leena.hrc.gmail.com>
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

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(image/png attachment: Screenshot_from_2018-10-03_20-19-44.png)

Received on Wed Oct 03 2018 - 08:30:02 PDT
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