[gmx-users] pdb2gmx parametrization of proteins consisted of metallo-bindings cofactor sites

James Starlight jmsstarlight at gmail.com
Fri Apr 22 17:00:09 CEST 2016

Dear Gromacs users!

I am interesting what full atomistic force field integrated in the
current GMX is better to use for the pdb2gmx parametrization of the
HEME containing proteins like cytochrome C (where cofactor is not
covalently bound to the polypeptide chain). e.g -ff amber 99sb did not
recognize HEM and -ff charm27 recognize it but have not found some
hydrogen atoms within HEM even -ignh was provided as well.
also I will be very thankful for refs to exact pdbs of the proteins
consisted of explicit metal bindings cofactor-sites which can be
processes using pdb2gmx without such problems + some particular
workflows (e.g how to rename cofactors within initial x-ray structure
prior to the pdb2gmx parametrization etc)!

Thanks for help!!


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