AMBER Archive (2007)

Subject: AMBER: NEB tutorial and addles

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Tue Mar 13 2007 - 22:28:20 CST

hi nall

I am trying to do the tutorial 5- The Nudged Elastic Band Approach to
Finding the Lowest Energy Pathway Between two States

and i am stuck at the addles part. The addles.out file is created but
it is empty. moreover, the other two files neb.prmtop and neb.inpcrd
which are supposed to form as output files are not created.

I dont know whats goin wrong with addles.though test runs are running.

another thing i would like to ask is the two end point conformations
that are made in addles, how are they made?i mean where can one change
the torsion angle atc to make a protein with different conformation.

any sugguestions in this regard are welcome as i am completely stuck.

thanks
deepti
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