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.
Mark
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