HI
I have attached Ubiquitin (Ub) C-term Gly to N-term Lys of a substrate protein via iso-peptide bond [C---NZ] (for ubiquitination) using Pymol and Coot. But when I do energy minimization, gromacs was supposed to alter isopeptide bond and make this bond into general peptide bond (Backbone) which I don't want.
I verified this bond initially and after EM by looking topology file also.
Could anyone write a suggestion, How can I resist isopeptide [C---NZ] bond through out simulation.
Your proteins need to be in separate chains (such that you can assign them their own NH3+ and COO- termini), and merge their moleculetypes together using pdb2gmx -merge in concert with a specbond.dat entry that defines the isopeptide bond. This should be created between custom residues, at least in the case of lysine. This topic has been addressed in full via gmx-users, so please search the archive there for previous, more detailed, solutions.
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