[Dock-fans] [Open Babel] UCSF Dock mol2 files

Scott Brozell sbrozell at rci.rutgers.edu
Tue Apr 3 12:13:01 PDT 2012


Hi,

This is a good suggestion.

But before implementation, 
1) do the DOCK developers or users have any comments ?
2) do the Chimera developers or users have any comments ?
  In particular, does Chimera use ########## as the lexeme for the DOCK token ?
  It might be useful to have a consistent lexeme across programs.
  Or maybe the Babel folks have comments on what would be a more general tag ?

thanks,
scott

On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote:
> Here you have two example files
> http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2
> http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2
> 
> What OB should do (in my mind) is to take "Name:" value as target molecule
> name and pass all 3 grid scores (total, vdw and ele) somehow (i guess
> comment is a right place, since there is not much choice), so that it can
> output it in simmilar manner.
> 
> Maybe it would be easier to have an option "d" (aka. dock) which would copy
> ALL the ###### data, and some other one, such as "s" (aka. sufix) to take
> suffixed name into account. Disadvantage of above is that it wouldn't work
> for other formats.
> ----
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> maciek at wojcikowski.pl
> 
> 
> W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison <
> geoff at geoffhutchison.net> napisał:
> 
> > > I have a thought about mol2 files form Dock program, which contain
> > > additional information in commentary (###). Those information is being
> > lost
> > > during openbabel operations, which is a pity. I'd like to propose a
> > in/out
> > > option for mol2 for Dock'ed mol2's to read/write compatible information
> > from
> > > those files. Especially conformer ID is important for further anylisis.
> > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg
> > files.
> >
> >
> > If you can give us a selection of example files and a list of what
> > information you'd like retained, it's fairly easy to patch the parsers.
> >
> > Cheers,
> > -Geoff


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