AMBER: Attaching capping groups

From: Neelanjana Sengupta <>
Date: Wed, 11 Apr 2007 18:28:33 -0700


I want to create alanine dipeptide by including the capping groups ACE and
CTE (see below) to the N-terminus and C-terminus of alanine. Do I need to
modify the leaprc file for this?
I am using amber7. I could not identify suitable terminal groups in the
all_aminoct94.lib and all_aminont94.lib.
Some advice is greatly appreciated.

'ACE' is (C=O)-(CH3)
'CTE' is (CH3)-(NH)

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 15 2007 - 06:07:14 PDT
Custom Search