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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 19 07:45:49 CET 2009

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.


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