Hi Tsjerk,<br><br>Sorry i did not supply any information about the enzyme/substrate system. Here, I'm studying the interaction between ester (substrate) and lipase (enzyme). The substrate contains C, O and H atoms. More details are shown in the following address.<br>
<a href="http://picasaweb.google.com/ZJULiuJi/Experiments#5304476447992943186">http://picasaweb.google.com/ZJULiuJi/Experiments#5304476447992943186</a><br>Also I'll check the archives for related topics. Thank you so much.<br>
<br>Ji<br><br><div class="gmail_quote">On Thu, Feb 19, 2009 at 6:18 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">
Hi Ji,<br>
<br>
Well, if others have been there before, you can of course take from<br>
their experience. You haven't mentioned the substrate you're dealing<br>
with, though, so none of us can tell if we can offer the solution to<br>
your problem. First try to search the user list archives and the<br>
topology contribution section of the gromacs site. If that doesn't<br>
give any results, you can post to the user list and see if any of us<br>
has already been there...<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="Wj3C7c"><br>
<br>
On Thu, Feb 19, 2009 at 10:35 AM, Ji Liu <<a href="mailto:zjuliuji@gmail.com">zjuliuji@gmail.com</a>> wrote:<br>
> Hi Tsjerk,<br>
><br>
> Thanks a lot.<br>
> Surely I can't modify the force field by my self. It's impossible to me to<br>
> understand all of things you mentioned. So is it the only way to achieve my<br>
> purpose? If so, it's so frustrating. I've been trying my best to contact<br>
> with the author of one of my references. He applied several of Gromos 96<br>
> force field (may be he modified these force field too) to a similar<br>
> enzyme/substrate system, and hope i can get some information from him. Even<br>
> though, i really eager to get some knowledge from all of gmx-users. Anyway,<br>
> I'm always grateful for your comment.<br>
><br>
> Ji<br>
> On Thu, Feb 19, 2009 at 5:09 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
>><br>
>> Hi,<br>
>><br>
>> > I'm not familiar with<br>
>> > i can't tell myself which<br>
>> > guess i can<br>
>> > I have no idea whether<br>
>><br>
>> This is the worst possible basis for trying to modify a force field.<br>
>> First get well acquainted with molecular dynamics and the role and<br>
>> whereabouts of force fields. Then you can start thinking of using such<br>
>> knowledge to modify the force field. You will possibly be able to<br>
>> change a force field, but making it produce sensible results is a<br>
>> different thing.<br>
>><br>
>> Sorry for not telling you what you want to hear.<br>
>><br>
>> Tsjerk<br>
>><br>
>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>> Junior UD (post-doc)<br>
>> Biomolecular NMR, Bijvoet Center<br>
>> Utrecht University<br>
>> Padualaan 8<br>
>> 3584 CH Utrecht<br>
>> The Netherlands<br>
>> P: +31-30-2539931<br>
>> F: +31-30-2537623<br>
>> _______________________________________________<br>
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<br>
<br>
<br>
</div></div>--<br>
<div><div></div><div class="Wj3C7c">Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
_______________________________________________<br>
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</div></div></blockquote></div><br>