AMBER Archive (2006)

Subject: AMBER: GB simulation problem

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Fri Jun 30 2006 - 11:49:53 CDT

Hi Users:
I have been trying to run a simulation of two peptides (+3.0 unit charge each)
with the GB model but the peptides fly away from each other. In a resent
work of Dr. Yong Duan (j. mol. biol. (2006) 356, 1049-1063) they resolve the
problem by set up a distance restain of 30 A between the center amino acid of
each peptide (two peptides) in their simulation. Also they set up the
restrain to not take effect if the distance between the peptides were less
that 30 A. I don't have any experience doing distance restrain. Is possible
to set up this kind of distance restrain in AMBER 8 ???
Any help will be appreciated!!

Best regards

Anthony Cruz
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