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
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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
