Dear Gromacs Users: I was wondering if there is a way to introduce an intra-chain peptide bond between side chains of LYS1 and GLU30 of Pin1 WW domain (PDB ID: 1I6C, Model 1). I'm trying to check if additional stability can be acquired from cyclisation using MD simulation.
The distance between NZ of LYS1 and CD of GLU30 is 3.3A. How can I make them to be close enough to form a peptide bond, and even if I manage to get them close enough, how can I actually introduce a peptide bond? Should I add modified residue information to somewhere? Thanks in advance! Best regards, Semin
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