Adding Hydrogens to PDB files

Pedro Coutinho coutinho at
Fri Oct 24 09:17:03 EST 1997


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

Pedro M. Coutinho                       Postdoctoral
CERMAV - CNRS                           Phone: +33-4 7603 7643 
BP 53 - 38041 Grenoble cedex 9          Fax:   +33 4 7654 7203
FRANCE                          Email:
coutinho at                              

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