RE: AMBER: Attaching capping groups

From: Ross Walker <>
Date: Wed, 11 Apr 2007 20:49:36 -0700

Dear Neelanjana,
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
mol = sequence { ACE ALA NME }
saveamberparm mol prmtop inpcrd
will accomplish what you want to do.
Good luck...

|\oss Walker

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From: [] On Behalf Of
Neelanjana Sengupta
Sent: Wednesday, April 11, 2007 18:29
Subject: AMBER: Attaching capping groups


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
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Received on Sun Apr 15 2007 - 06:07:14 PDT
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