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
____________________________________________________________________________
Received on Wed Feb 19 2003 - 00:02:30 PST
