RE: AMBER: new aminoacid

From: Ross Walker <>
Date: Mon, 17 Jan 2005 10:34:05 -0800

Dear Gustavo,
If you look at the following tutorial it details how to use xleap to create
a non-standard residue. In the case of the tutorial a copper bound
histidine. You could easily adapt this for your non-standard amino acid.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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From: [] On Behalf Of
Gustavo Pierdominici Sottile
Sent: 17 January 2005 08:27
Subject: AMBER: new aminoacid

Hi, I am trying to make leap recognize the pdb input that has a non-
standard aminoacid. I have made the .in file, an have already developed the
parameters. The problems is that when I load the input.pdb the parameters
that are absents are not what they should be. For example, it appears that a
CW-C bond is absent, but I have not this bond in the non standard aminoacid.
The question is the following: should I add other information besides .in
file? I believe that the connection information is wrong, and should add
this new aminoacid to the file all_amino94.lib
Thanks in advance

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Received on Mon Jan 17 2005 - 18:53:01 PST
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