AMBER: Error in protonating

From: Neelanjana Sengupta <>
Date: Fri, 27 Apr 2007 04:31:52 -0700

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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Apr 29 2007 - 06:07:34 PDT
Custom Search