Re: adding_hydrogens_to_pdb (fwd)

From: David A. Case <>
Date: Mon 26 Aug 2002 17:34:36 -0700

On Mon, Aug 26, 2002, 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:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Aug 26 2002 - 17:34:36 PDT
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