Dear Amber users!
I am interesting in param set which should I use in tleap input file
for proper recognition within given PDB of some buried metalo-binding
cofactors (not covalently bound to the polypeptide chain) like in case
of Cythochrome-C (HEM with Fe).
Also could someone recommend me simple preparation workflow for any of
Metal-binding proteins (even without of additional cofactors like
Calmodulin). E.g typically I use pdb2pqr to prepare PDB prior to the
tleap parametrization which is unfortunately remove all ions from the
initial pdb. Is it method to present it within buried protein sites
and parametrize properly using some amber param-set?
Thanks for help!
James
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Received on Wed Apr 27 2016 - 02:30:03 PDT
