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

Ji Liu zjuliuji at gmail.com
Thu Feb 19 09:08:46 CET 2009

Hi Mark,

Thank you for your suggestion. As you know, I'm not familiar with the force
field so i can't tell myself which one of the available force field is
suitable to me. Fortunately, I find the force field Gromos96 and Amber have
been adapted in previous studies. So guess i can use these kind of force
fields too, 'cuase I have very similar system with those in other studies.
I'm working with Gromos96, trying to generate the pdb file of substrate from
Prodrg server and combine it with the enzyme file. I have no idea whether it
can work. Would you help me with your suggestion?
Thank again.


On Thu, Feb 19, 2009 at 2:45 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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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