Ji Liu wrote:
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.
Your first question is to work out if there exists a force field
suitable for modeling your enzyme-bound-substrate system. This may not
be an easy question to answer, or a question whose answer you like. Only
then do you need to worry about whether pdb2gmx can be persuaded to
generate a topology for it.
Mark
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