Ji Liu wrote:
Hi Tsjerk,
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.
http://picasaweb.google.com/ZJULiuJi/Experiments#5304476447992943186
Also I'll check the archives for related topics. Thank you so much.
Based on the structure you've shown, I do not believe there is any easy
solution, other than going through the painstaking progress of deriving new
force field parameters. It doesn't matter so much which atom types are used in
your case, but how they are linked. An ester adduct such as you've shown has
not been parameterized within the Gromacs implementation of Gromos96. If other
researchers have done it, then your best bet is to see how they did it and
hopefully apply it to your situation.
Otherwise, you have a long project ahead of you just to derive the correct
parameters.
-Justin
Ji
On Thu, Feb 19, 2009 at 6:18 PM, Tsjerk Wassenaar <tsje...@gmail.com
<mailto:tsje...@gmail.com>> wrote:
Hi Ji,
Well, if others have been there before, you can of course take from
their experience. You haven't mentioned the substrate you're dealing
with, though, so none of us can tell if we can offer the solution to
your problem. First try to search the user list archives and the
topology contribution section of the gromacs site. If that doesn't
give any results, you can post to the user list and see if any of us
has already been there...
Cheers,
Tsjerk
On Thu, Feb 19, 2009 at 10:35 AM, Ji Liu <zjuli...@gmail.com
<mailto:zjuli...@gmail.com>> wrote:
> Hi Tsjerk,
>
> Thanks a lot.
> Surely I can't modify the force field by my self. It's impossible
to me to
> understand all of things you mentioned. So is it the only way to
achieve my
> purpose? If so, it's so frustrating. I've been trying my best to
contact
> with the author of one of my references. He applied several of
Gromos 96
> force field (may be he modified these force field too) to a similar
> enzyme/substrate system, and hope i can get some information from
him. Even
> though, i really eager to get some knowledge from all of
gmx-users. Anyway,
> I'm always grateful for your comment.
>
> Ji
> On Thu, Feb 19, 2009 at 5:09 PM, Tsjerk Wassenaar
<tsje...@gmail.com <mailto:tsje...@gmail.com>> wrote:
>>
>> Hi,
>>
>> > I'm not familiar with
>> > i can't tell myself which
>> > guess i can
>> > I have no idea whether
>>
>> This is the worst possible basis for trying to modify a force field.
>> First get well acquainted with molecular dynamics and the role and
>> whereabouts of force fields. Then you can start thinking of
using such
>> knowledge to modify the force field. You will possibly be able to
>> change a force field, but making it produce sensible results is a
>> different thing.
>>
>> Sorry for not telling you what you want to hear.
>>
>> Tsjerk
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>> _______________________________________________
>> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>
>
> _______________________________________________
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>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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