[gmx-users] cyclic peptide dynamics. peptidic bond

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 24 17:25:17 CEST 2006

Giacomo Bastianelli wrote:
> I have been changing manually all the topology files 
> (from the bonds, angles ecc...) but I constantly find
> fatal errors during the minimization (example: atoms 
> do not match, ecc..). I guess that it is really demanding
> and difficult to change manually the topology file to have
> gromacs recognizing a peptide bond that cyclize a protein.
> any suggestion?

Follow Tserk's advice! As an easier exercise, try writing down all of 
the bonded and pair interactions that should defined for a given 
forcefield for a glycine dipeptide. Then compare with what pdb2gmx 
produces. Work out what you got wrong. This will teach you how to make a 
peptide bond. Then go and make a cyclic peptide bond.


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