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 - 02:30:03 PDT
