AMBER Archive (2006)

Subject: Fw: AMBER: HBOND ANALYSIS

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Sat Aug 05 2006 - 14:45:10 CDT

----- Original Message -----
From: "Claire Zerafa" <cporteli_at_waldonet.net.mt>
To: "amber" <amber_at_scripps.edu>
Sent: Friday, August 04, 2006 4:35 PM
Subject: AMBER: HBOND ANALYSIS

> 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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu