AMBER Archive (2009)

Subject: [AMBER] missing violations of the covalent geometry

From: Helena P M Tossavainen (haitio_at_cc.helsinki.fi)
Date: Tue Apr 07 2009 - 04:36:44 CDT

Dear Amber users,

After a successful simulated annealing run I obtain the list of NMR
restraint violations, made by the LISTOUT=POUT command. However, the lines
"RMS deviation from ideal bonds/angles" are missing. I am currently
running sander in Amber 10. Using the same input file with Amber 8
produces these lines in the output. How should the input file be modified
to get these lines? Or is there an other method to analyze covalent
geometry violations?

Many thanks,

Helena Tossavainen
Institute of biotechnology
University of Helsinki
Finland

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