AMBER Archive (2002)

Subject: Re: adding_hydrogens_to_pdb (fwd)

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 26 2002 - 19:34:36 CDT

On Mon, Aug 26, 2002, amber_at_heimdal.compchem.ucsf.edu wrote:
>
>
> I'm searching for a program adding hydrogens to (xray) pdb files.
> As far as I can see the program AMBER can do this job.
> Can you tell how does the program calculates the koordinates of the
> protons to be added ?
>

The "protonate" program uses a set of rules (in the PROTON_INFO file) that
build the H's relative to the nearby heavy atom positions. This is pretty
good for non-polar hydrogens. The "pol_h" program will attempt to optimize
the positions of polar protons, esp. OH groups.

Neither program is perfect: we mainly use this to get started...the "real"
positions arise from equilibration.

..hope this helps...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================