[gmx-users] topology for protein-surface amide bond

Jon jon.ellis at utoronto.ca
Wed Aug 17 16:36:02 CEST 2005

Dear GMX-users

I want to make an explicit amide bond between a lysine-group amine on a 
protein and a -COOH head on an alkyl surface. I have separate topologies 
and equilibration trajectories for both the protein and the surface. 
I've identified the alkyl chain I want to bind to and oriented the 
protein so the amine is the correct distance from the COOH. I removed 
the amine hydrogens from the protein and the OH from the carboxylic acid 
in the .gro file.

What is a good way to combine the topologies to include the explicit 
bond? Can I just combine two .itp files in a singles topology? If so how 
do I make the explicit bind and what atom numbers do I use? Or should I 
just renumber either the protein or the alkyl surface topology, and then 
combine the two in one big .top file?

Or am I completely missing something, and does somebody have a better 


Jon Ellis
PhD Candidate, Thompson Group
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
University of Toronto
LM147 - (416) 978-6568
jon.ellis at utoronto.ca

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