Problem with Protonate

From: Jithesh P.V <>
Date: Sat 29 Jan 2000 13:32:57 +0530 (IST)


I'm facing a little problem with Protonate (Amber 5). I'm trying to
protonate a DNA PDB file from the Protein Data Bank with the following

protonate -k -d ~/AMBER/dat/PROTON_INFO <dna.pdb> dna.pdb.h

But it's not adding any hydrogen and the Edit program finds it difficult
to fix some of the hydrogens placing them far from the molecule.
But if i use the PROTON_INFO.Brook file it's adding hydrogens except H5T.
I'll have to again modify this file to make it as an Edit input.

To my surprise, the Protonate program is working nicely with protein PDB
files evenif PROTON_INFO is used.

Can you please help me to solve the problem?
Thanks in advance.


Jithesh P.V.
Engineer Trainee
National PARAM Supercomputing Facility
Centre for Development of Advanced Computing
Pune University Campus, Pune, India - 411007.
email :
Received on Sat Jan 29 2000 - 00:02:57 PST
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