From: Steve Seibold <>
Date: Wed, 10 Jan 2007 11:46:28 -0500

Hello Amber

I have a crystal structure of a large enzyme (resolution ~
2.5Angstroms). When up load my structure (without hydrogens) in to
xleap, xleap then adds hydrogens to my structure. However, it then tells
me when I do a "check" unit that the hydgrogens it has added are
"Warning: Close Contact" between atoms of the protein and the hydrogens
it has added. There are 170 warnings of this kind. I have tried to
energy minimize the structure, but it is proving to be very, very
difficult with the repeat warning (in sander during minimization)
"repeated limit failure" and stops the minimization. I have tried every
routine (i.e. different strategies for minimization..i.e. different
ncycle and maxcycle) and nothing is working. Can you some one give me
some advice?


Thanks, Steve



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Received on Sun Jan 14 2007 - 06:07:11 PST
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