[Dock-fans] amber score in dock 6.1 (Yubo Fan)

Devleena devleena at scripps.edu
Mon Dec 3 11:16:21 PST 2007


Hi Yubo,

You need to use the nab_atom_expression for that purpose.
Check AMBERScore section in DOCK 6 manual:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
For ex, if your ligand is strand 2 and protein is strand 1, the
nab_atom_expression for ligand and residue 20-30 flexible would
be: 2::|1:20,21,22,23,24,25,26,27,29,30

Hope this helps.

Devleena

> ------------------------------
> 
> Message: 5
> Date: Thu, 29 Nov 2007 13:38:17 -0600
> From: "Yubo Fan" <yubofan at mail.chem.tamu.edu>
> Subject: [Dock-fans] amber score in dock 6.1
> To: <dock-fans at docking.org>,	<CHEMISTRY at ccl.net>
> Message-ID: <001001c832bf$63efee70$94b25ba5 at yubopcatlab>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hello,
> 
> I have a question about setting the flexible region for docking with UCSF Dock 6.1.
> 
> If I need to set the ligand and certain amino acid residues as movable
> region, how can I define them. For example, how can I set the ligand and
> residue 20-30 movable for docking in the keyword shown below? 
> amber_score_movable_region [ligand] (distance, everything, ligand,
> nab_atom_expression, nothing): 
> 
> Thanks a lot,
> 
> Yubo
> ============================================================
> Yubo Fan  Ph.D             Email: yubofan at mail.chem.tamu.edu
> Department of Chemistry    Tel:   1-979-845-5237
> Texas A&M University
> College Station, TX 77843
> ============================================================



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