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.
Try
which protonate
which PROTON_INFO
If you try the following it will likely work:
$AMBERHOME/exe/protonate -d $AMBERHOME/dat/PROTON_INFO <peptide.pdb >
peptide2.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
Ross
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Neelanjana Sengupta
Sent: Friday, April 27, 2007 04:32
To: amber.scripps.edu
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.
Thanks,
--
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta.uci.edu
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Received on Sun Apr 29 2007 - 06:07:37 PDT
