Hello everyone, I'm gonna run MD simulation with a enzyme/substrate system. Here the substrate must connected with the side chain of an activity residue of enzyme through covalent bond. However, i really have no idea about the preparation of such a complex structure file. Actually, i tried to modify the pdb file to combine the substrate and enzyme, but it seemed that pdb2gmx can no t process the substrate part in the structure. So much thanks for your suggestion.
Liu Ji
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