AMBER Archive (2003)

Subject: Adding ACE to chopped protein

From: Karl N. Kirschner (crux5_11_at_yahoo.com)
Date: Wed Apr 16 2003 - 15:08:45 CDT

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
atom."

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
advance...

Cheers,
Karl

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