ADL: convert planner pdb file to 3d

Kim Branson kim.branson at
Sat Feb 19 00:11:15 PST 2005

Hash: SHA1

hi yuchen

there are a few ways of building 3d coordinates for your files.

1. concord (distributed by Tripos)
2. Omega (open eye scientific) you may qualify for an academic no cost 
licence :)  You might also be able to use their web demo site....
3. randomly giving the atoms a number (not too huge, but make sure they 
are not on top of each other, and reasonable) and using a free 
MD/minimisation  package like TINKER might be good. (i've never done 
this but it might work)
4. CORINA,  you can do 1000 structures for free.



On 19/02/2005, at 6:37 PM, yangyc at wrote:

> dear all,
> i have a question which is not really about autodock...
> i downloaded some small molecule pdb files from chemIDplus from NIH, 
> but
> found that all the pdb files are planner. To be detailed, the z-axis
> values are all 0.
> i tried to use the Dundee PRODRG2 Server to convert the planner pdb 
> file
> into 3D, but not sure if the converted results are reliable. so if 
> anyone
> have tried any other softwares for such 2D-to-3D convertion of chemical
> structures, could you please tell me about that?
> thanks a lot!
> cheers,
> yuchen
> ________________________________________________
> --- ADL: AutoDock List  --- 
> ---
Dr Kim Branson
Peter Doherty Fellow
Protein Structure and Function
St Vincents Institute for Medical Research
41 Victoria Parade, Fitzroy
Victoria 3065, Australia.
Phone: +613 9288 2480
Fax: +613 94162 676
Ph +613 9662 7136
kbranson at
kim.branson at
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