ADL: python error Herlp Requested

Rudy J. Richardson rjrich at umich.edu
Tue Sep 7 10:09:33 PDT 2010


Phil:

Have you tried upgrading to the latest version of autodock?

In addition, I would recommend adding hydrogens first, then merging 
hydrogens, then computing Gasteiger charges.

--Rudy

On Mon, 6 Sep 2010, Phil Cunningham wrote:

> Hi
> I havent used adt for a wee while and am having trouble .....
>
> I am using a Model protein
> I am using SUSE linnux 9.2
> and ADT with Autodock 3.0.5
>
> the problem -
> I read the protein
> Load /repair missing atoms
> edit charges / compute gasteiger / check totals on residues ? spread on all 
> atoms
> edit hydrogens  / add polar only
> Save /write PDB file
>
>
> WHen I come to generating the pdbqs file (from grid /macro molecule choose)
> I get a python error report
>
> I have tried this a number of times in various combinations and cant see the 
> error of my ways
>
> Perhaps you would be able to advise me on a way forward
>
> The python error report with both the source and the generated pdb files 
> attached
>
> many thanks
>
> Phil
>
> -- 
> Phil Cunningham
> Senior Bioinformatics Officer
> Room 3.157 Franklin Wilkins Building
> Department of Biochemistry
> King's College University of London
> 150 Stanford Street
> London SE1 9NH
>
> tel 020 7848 4239
> fax 020 7848 4500
>
> email phil.cunningham at kcl.ac.uk
>
>


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