Adding Hydrogens to PDB files

islam islam at icrf.icnet.uk
Mon Oct 27 11:27:03 EST 1997

Hi, I have a program (call genhydpdb) which will generate hydrogen
atoms given a PDB file. In addition, for residues with rotatable
hydrogen atoms (e.g. OH-tyr) it can (as an option) generate all
possible (practically speaking a number of rotated conformers)
conformers. At present it writes out all the various conformers,
but it should be a simple step to search for local hydrogen
bonds and only write out appropriate H atom positions. Please
email me if you are interested in the program. I have binaries
for Silicon Graphics Irix5.2-6.3.
Suhail A Islam
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund, P.O. Box 123
44 Lincoln's Inn Fields, London WC2A 3PX
Tel: (0171) 269 3380, Fax: (0171) 269 3479
email: islam at icrf.icnet.uk

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

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