[Dock-fans] ligand -regding

Vinay Kumar ksvinaykumar at gmail.com
Sun Dec 2 00:43:33 PST 2007


Hi again,
I use MDL ISIS draw (free) software for drawing my ligands, save it,
and port it through Babel, which would give me, mol2 or pdb output
files, which i can use as input ligand file in DOCK. i hope this is
what was asked for!! (and please tell me, if my method mentioned above
is ok?)

is there anyway, i can know, what scoring function is in use, and can
i change it in DOCK?

With regards,
Vinay


On Dec 2, 2007 11:16 AM, John J. Irwin <jji at cgl.ucsf.edu> wrote:
> Hi Vinay
>
> It would be helpful for you to tell us a bit more about what program(s)
> and options you are using. Which version of docking software? Which
> drawing interface?
>
> In general, if you are using a united-atom scoring function, then you
> only want polar hydrogens on the protein. If you are using an all atom
> scoring function, then you will need all H atoms to be explicit. You
> always need (at least for all versions of DOCK) a ligand with all atoms
> explicitly represented, for example as found in ZINC.
>
> Good luck
>
> John
> johnirwin.docking.org
>
>
>
> Vinay Kumar wrote:
> > Hello dockers,
> >
> > I would like to know,
> > 1) why is it that only polar hydrogens are added in the macromolecule?
> > 2) if we need to add all hydrogens (polar and non-polar) explicitly to
> > the ligand while a docking is performed? for ex- if the ligand is
> > phenol, do i have to draw the phenyl ring with CH2 explicitly shown,
> > or just use the ring structure provided by the drawing interface?
> >
> > would like your thoughts,
> >
> > regards,
> > Vinay
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
>


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