AMBER Archive (2006)

Subject: AMBER: HBOND ANALYSIS

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Fri Aug 04 2006 - 09:35:50 CDT

Dear Amber Users,

I have carried out hbond analysis on an androgen receptor (pdb 1e3g)
bound to 4 different ligands (2 steroidal and 2 non-steroidal). I get
results that are consistent with those quoted in literature, for all of
my complexes, except for the case in which the receptor is bound to the
non steroid vinclozolin. Here, no hbonds are found over a 4820 ps
trajectory between the ligand and the active site amino acids. I want to
verify that this is indeed the case- ie that the fact that no hbonds are
being observed is not due to default cutoffs. It has been suggested to
me that I could constrain hbonds, re-run some dynamics and repeat the
hbond analysis. I am not quite sure how to go about this, and would
appreciate some help.

Thanks in advance

Claire

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