How can I generate a topology for a peptide contain unnatural amino acids and a flexible linker?

29 August 2022 0 3K Report

Dear All,

I want to generate topology files for the following peptide having an aliphatic linker in the middle and an unnatural amino acid to perform MD simulation using GROMACS. I tried to generate these (.itp ) files using CHARMM-GIU, but I do not know how to get topology and parameter files for the unnatural amino acid and the aliphatic linker.

Can anyone know how to generate these files?

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