Adding Hydrogens to PDB files

Simon C. Lovell lovell at iris.biochem.duke.edu
Mon Oct 27 12:39:56 EST 1997

Pedro Coutinho wrote:
> Hello!
> As we know, many files in the PDB don't have coordinates for hydrogen
> atoms. This can be a limitation when using these files to study the
> interaction with different ligands.
> Presently I am looking for software to add hydrogens (or corrects their
> positions) to PDB files that takes in account H-bonding. Most programs
> place the hydrogens in fixed positions relative to the side-chains. This
> can be a problem in placing polar hydrogens in groups like Tyr, Thr,
> Ser, etc...
> As an example of problems found in adding polar hydrogens in this fixed
> geometry mode, Sybyl and HBPLUS add hydrogens to the OH group of Tyr in
> a opposite position relative to the CZ-OH bond! This is equivalent to a
> rotation of 180 degrees around that bond that is probably not leading to
> the same minima upon minimization!
> When dealing simultaneously with different PDB files it is very
> difficult to manually check these assignments...
> Any ideas?!
> Thank you,
> Pedro Coutinho

We use the hb2 module in whatif to position polar hydrogens, and our own
program 'reduce' to add the others geometrically. Reduce is available
from our ftp server (suna.biochem.duke.edu in  /pub/UNIXprograms).
Contact me if you want more details.


Dr Simon Lovell, 211 Nanaline Duke Buillding,
Biochemistry Dept, Duke University, NC 27710, USA.
Enzymes are things invented by biologists that explain things which
otherwise require harder thinking. -- Jerome Lettvin

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