ADL: docking results not very accurate

snoze pa at
Thu Jan 31 12:24:00 PST 2008

Best advice? try to recalculate the charges,  use antechamber to calculate
the charges if you do not have gaussian. I know this prob is common but you
can get better binding energy and conformation. But end of the day, analysis
is more important.

On Jan 31, 2008 12:33 PM, Wilfred Li <wilfred at> wrote:

> I'd consider it reasonable if your 2nd best binding energy contains your
> best pose. Would you have been able to select this cluster using some
> other criteria, such as most populated cluster? Changing the rmsdtol may
> also help. There are other settings to tweak, but you seem getting
> close. There are no attachments, btw.
> Regards,
> Wilfred
> -----Original Message-----
> From: autodock-bounces at [mailto:autodock-bounces at]
> On Behalf Of Fabian Glaser
> Sent: Thursday, January 31, 2008 12:40 AM
> To: autodock at
> Subject: ADL: docking results not very accurate
> Dear Autodock colleagues,
> I'd be very grateful for any advice with the following:
> I am trying to perform docking experiments for a colleague. Initially I
> have performed several experiments trying to re-dock the co-crystallized
> ligand (the structure is 1nex, and the ligand, a modified peptide), to
> check the procedure, and later the idea is to use the same procedure to
> dock a peptide that they think represents the substrate on a modelled
> structure.
> The problem is that when I try to dock the co-crystallized ligand (as an
> initial test), the "correct" result does not appear in the best energy
> cluster: Attached figure snapshot3.png shows the best energetic cluster
> found within 100 docked results, and snapshot2.png the second best
> cluster, which is the correct  one (in blue the protein, in green the
> co-crystallized ligand, the docked ligand is colored by element). The
> different clusters are shown in the small figure on the right, in blue
> bars.
> I am quite a rocky with docking, so any help how can I improve these
> results will be highly appreciated.
> Best regards and thanks a lot in advance.
> Fabian
> --
> Fabian Glaser, PhD
> Bioinformatics Knowledge Unit,
> The Lorry I. Lokey Interdisciplinary
> Center for Life Sciences and Engineering Technion - Israel Institute of
> Technology Haifa 32000, ISRAEL
> E-mail: fglaser at
> Tel:   +972-(0)4-8293701
> Cel:   +972-(0)54-4772396
> -
> ________________________________________________
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