Adding ACE to chopped protein

From: Karl N. Kirschner <>
Date: Wed, 16 Apr 2003 13:08:45 -0700 (PDT)

Hello Amber community,
  This email concerns adding terminal groups to a
protein fragment using leap.
  I have a large protein that I chopped in half - the
second half being the interesting part. The sequence
starts with a PRO residue and is mapped as a NPRO
using leap. What I would like is the have ACE and the
starting residue. I have tried the following commands
in leap, which have lead to nothing but frustration:

>X = loadpdb protein.pdb
>Y = sequence { ACE X }

This give the following error:

"One sided connection. Residue: missing connect0

So, I did
>addPdbResMap { { 0 "PRO" "PRO" } }
>X = loadpdb protein.pdb
>set X head PRO.1.N
>Y = sequence { ACE X }

I received the same message and looking at the
structure (edit Y) shows only the ACE.

Do you see what I am doing wrong? Any ideas on how to
add an ACE residue to an existing pdb file? Thanks in


Karl Nicholas Kirschner, Ph.D.
National Institute of Health Fellow
Complex Carbohydrate Research Center
University of Georgia - Athens, Ga USA

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Received on Wed Apr 16 2003 - 21:53:01 PDT
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