Dear All I have a protein where one residue ( Lysine ) is making a covalent bond with the cofactor Pyridoxal phosphate. I have created other parameters of heteroatom PLP through PRODRG and manual checking. But I am not sure how to include the parameters for the "imine" bond ( C=N bond ) that has been formed between side chain amine group of lysine and aldehyde group of Pyridoxal phosphate. Do I have to edit C-termini database file ( ff????-c.tdb ) ? A clue to this problem will be highly appreciated. Regards Supti Mukhopadhyay Senior Research Fellow Department of Psychopharmacology NIMHANS, Bangalore India
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