AMBER Archive (2005)

Subject: RE: AMBER: new aminoacid

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jan 17 2005 - 12:34:05 CST

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.
 
see:
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/index.htm
 
All the best
Ross

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Gustavo Pierdominici Sottile
Sent: 17 January 2005 08:27
To: amber_at_scripps.edu
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
Gustavo

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