AMBER Archive (2006)

Subject: Re: AMBER: adding polar hydrogens

From: Sean Rathlef (
Date: Wed Oct 11 2006 - 13:02:28 CDT

From: "David A. Case" <>
> Some more information would help a lot:
> 1. What is in "out.pdb"?

> 2. Which version of Amber? (I'm assuming this is cygwin(?); which
As noted, I'm using just the protonate.exe from Autodock. THis was in my
original two emails, and you suggested I ask on the Amber reflector

> 3. Do you have the $AMBERHOME environment variable set correctly?
I'm not using Amber

> 4. Is the PROTON_INFO file empty? (That would suggest that $AMBERHOME is
not set correctly.)
Yes, it is empty.

> > Do I need to use PROTON_INFO.kollua_polH, as in:
> > protonate.exe -k PROTON_INFO.kollua_polH < name.pdb > out.pdb
> If you want to use this file, which I assume you made yourself, then you
> certainly need to specify it with the "-d" flag.
The README for the PROTON_INFO.kollua_polH says it was written by David Case
and Garry Gippert. It is located in the \src\protonate directory.

Excerpt from README


This is a utility written by David Case and Garry Gippert to add hydrogens
to a molecule.

Use '.kollua_polH' polar-Hydrogens for docking studies.


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