Date: Mon, 26 Aug 2002 17:34:36 -0700
From: "David A. Case"
Subject: Re: adding_hydrogens_to_pdb (fwd)

On Mon, Aug 26, 2002, amber@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