RE: AMBER: Error in protonating

From: Ross Walker <>
Date: Fri, 27 Apr 2007 08:46:50 -0700

Dear Neelanjana,
Do you have gromacs installed on this machine? I suspect your paths are set
in such a way that you are not running what you think you are running.
which protonate
If you try the following it will likely work:
$AMBERHOME/exe/protonate -d $AMBERHOME/dat/PROTON_INFO <peptide.pdb >
Also take a look at peptide.pdb and see if it looks to be a valid pdb file -
I.e. one that adheres to the PDB standard.
All the best
|\oss Walker

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From: [] On Behalf Of
Neelanjana Sengupta
Sent: Friday, April 27, 2007 04:32
Subject: AMBER: Error in protonating

Dear Amber users,

In protonating a peptide (coordinates available in pdb format), I use the
foll. command:

protonate -d PROTON_INFO < peptide.pdb > peptide2.pdb

and, I get the foll. error:

:-) G R O M A C S (-:
Segmentation fault

The peptide2.pdb does get created, but is a blank file. Could someone point
out what's missing here? I am using amber7.

Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921
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Received on Sun Apr 29 2007 - 06:07:37 PDT
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