[Dock-fans] amber score final pose

Floris Buelens floris_buelens at yahoo.com
Fri Oct 6 03:42:12 PDT 2006


I'm running Amber MM/GBSA scoring jobs using Dock6, with localised receptor flexibility in the binding site, and have an issue regarding the final minimised conformations. As referenced in the message quoted below, the final conformation after MD and minimisation should be written out to the scored ligand mol2 file, and also a pdb file ending final_pose.pdb. Although both of these files are written, and although the scored ligand mol2 file includes the final score, the final conformations are not written - i.e. the protein and ligand conformations of the input ligand mol2 file, the input receptor pdb file, the scored ligand mol2 file, and the final_pose complex pdb file, are all identical. Does this work for anyone else? Is there any way to resolve this?

Floris Buelens
Crystallography, Birkbeck College, London

[Dock-fans] Re: DOCK6 amber score
    Terry Lang 
    terry at cgl.ucsf.edu

    Fri Jul 21 17:48:18 PDT 2006
    Previous message: [Dock-fans] dock6 compilation problems (gfortran)
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Dera Keng-Chang,

1) Delphi is a third party program. It can be obtained from the Delphi
web site at http://honiglab.cpmc.columbia.edu/delphi/.

2) You do get the induced-fit ligand-receptor structure after scoring.
Once you have completed a scoring run, you should get a file labeled:


where XXX = name of receptor used for prepare_amber.pl
YYY = name of ligand library used for prepare_amber.pl
# = index in ligand library of ligand being scored

The outputted pdb file has the final conformation of both the receptor
and the ligand.


> Sincerely,
> Keng-Chang Tsai,Ph.D.
> The Genomics Research Center, Academia Sinica,Taiwan
> 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan
> tkc at gate.sinica.edu.tw <mailto:tkc at gate.sinica.edu.tw>

P. Th
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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