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

David spoel at xray.bmc.uu.se
Wed Aug 17 16:50:13 CEST 2005

On Wed, 2005-08-17 at 10:36 -0400, Jon wrote:
> 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?

try adding it to specbond.dat  and run pdb2gmx

> Or am I completely missing something, and does somebody have a better 
> suggestion?
> Cheers
> Jon
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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