From: Maria Lin (mar_lin_at_uclink.berkeley.edu)
Date: Tue Jun 14 2005 - 14:03:59 CDT
Question on meaning of poorly guessed coordinates
NAMD Tutorial: After making the ubq.psf and ubq.pdb, the Terminal screens had "Warning: Poorly
guessed coordinates." The tutorial does not talk much about these warnings and I would like to
know what it means by poorly guessed coordinates. When we do run this program using another
protein, are we inputting info for the coordinates and running it until vmd says we have correctly
guessed coordinates?
Also, what are the purpose of creating chains? (referring to page 10) in the tutorial.
Thank you for your time and help. Please email me back :)
Maria Lin
mar_lin_at_berkeley.edu
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