Dear Hannes and Bill,
Thanks for your valuable suggestion. The xleap and reduce didn't help much
as the compound library is not in the database.
However the suggestion to use OpenBabel worked.
Jac
On Tue, Apr 18, 2017 at 2:52 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk
> wrote:
> On Tue, 18 Apr 2017 14:27:34 +0530
> jacob wick <jacobwick.la.gmail.com> wrote:
>
> > Dear all,
> >
> > I have a library of compounds which do not have explicitly added
> > Hydrogens. The data is in .sdf or .pdb file formats.
> > Can some amber module be used to do this? If so, please guide.
>
> There is reduce which can add hydrogens to PDB files. For arbitrary
> small molecule ligands this however only works when they are in
> reduce's database. So you may want to look into external toolkits like
> OpenBabel or RDKit, for example. But keep in mind that those only fill
> missing valencies based on the bond order. Depending on your data set,
> you may have to consider protonation states as well as tautomeric states
> but there is no general solution to this problem.
>
> Cheers,
> Hannes.
>
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Received on Tue Apr 18 2017 - 03:30:02 PDT
