AMBER Archive (2003)

Subject: Re: adding hydrogens

From: Oliver Hucke (Oliver.Hucke_at_physchem.uni-freiburg.de)
Date: Wed Feb 19 2003 - 02:02:30 CST

Hi Guanglei,

I can recommend the HB2NET command of WhatIf which searches for the
optimal hydrogen bonding NETWORK as a basis for hydrogen placement.
The corresponding reference is:

@article{70012,
   author = {R. W. W. Hooft and C. Sander and G. Vriend},
   title = {Positioning hydrogen atoms by optimizing hydrogen-bond
networks in protein structures},
   journal = {Proteins},
   volume = {26},
   pages = {363-376},
   year = {1996},
   keywords = {Hydrogen bond ; protein ; Protein Structure ; Structure ;
hydrogen modelling ; whatif}
}

Hope this helps.
Kind regards,

Oliver

"CUI, Guanglei" wrote:
>
> Dear all,
> I'm trying to do some pKa calculations with amber force field. Can
> anyone recommend a good program to add hydrogen atoms to PDB files?
> I know protonate can do it, but I have non-amino-acid residues
> protonate doesn't know how to deal with.
>
> --
> Guanglei Cui
> Dept. of Chemistry
> SUNY at Stony Brook
> Stony Brook, NY 11790 

-- 
____________________________________________________________________________

Dr. Oliver Hucke
Inst. fuer Physikalische Chemie II
Universitaet Freiburg
Albertstr. 23a
D-79104 Freiburg

Tel. :  +49-761-203-5130 (/-6179)
Fax. :  +49-761-203-6189
email:  Oliver.Hucke_at_physchem.uni-freiburg.de
____________________________________________________________________________