ADL: Prepare all parameters

Sargis Dallakyan sargis at scripps.edu
Mon Jan 28 11:44:15 PST 2008


Jack Shultz wrote:
> Great one other thing, may be trivial, certain pdb files will generate PDBQT
> with a substring "model1", any idea what is going on there?
> 
> C:\Program Files\MGLTools
> 1.4.6\MGLToolsPckgs\AutoDockTools\Utilities24>prepare_all4.py
> -l nsc2559.mol2 -r 1txe.pdb
> 01/28/2008  02:21 PM            65,315 1txe_model1.pdbqt
> 01/28/2008  02:21 PM             3,669 nsc2559.pdbqt
>                3 File(s)         69,819 bytes
>                0 Dir(s)  18,727,534,592 bytes free

My guess is that 1txe.pdb is NMR with multiple models and prepare_all4.py 
creates pdbqt for the first model. I think prepare_ligand does similar thing; if 
you pass pdb with multiple molecules, and '-v' option, it prints "more than one 
molecule in file" and which molecule it selected.

-Sargis


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