Dear Amber Users,
I wanted to generate a average structure form 1
ns trajectory file of my protein using 'average' command of ptraj. My input
file is like following:
trajin protein_prod_1ns.mdcrd
average protein_prod_1ns_avg.pdb pdb
When I observe my pdb file of average structure I noticed that some portion
of protein is very unstable and very absurd. Atoms are overlapping and some
unusual bonds are also present. Then, I followed analysis portion of
TUTORIAL B3. Here also structure is like before. Some unusual bonds and
overlapped atoms are present. How can I overcome it? Please help.
Sanjib
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Received on Tue Aug 28 2012 - 07:30:03 PDT
