AMBER Archive (2005)

Subject: AMBER: new aminoacid

From: Gustavo Pierdominici Sottile (gsottile_at_unq.edu.ar)
Date: Mon Jan 17 2005 - 10:26:32 CST

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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