Hi Mark,<br><br>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. <br>
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?<br>Thank again.<br>
<br>JI<br><br><div class="gmail_quote">On Thu, Feb 19, 2009 at 2:45 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="Wj3C7c">Ji Liu wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello everyone,<br>
<br>
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.<br>
So much thanks for your suggestion.<br>
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<br></div></div>
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.<br>
<br>
Mark<br>
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