[gmx-users] Problem in preparation of the enzyme/substrate complex

Ji Liu zjuliuji at gmail.com
Thu Feb 19 07:15:50 CET 2009

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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