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

[Ji Liu]

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.

Ji

On Thu, Feb 19, 2009 at 6:18 PM, Tsjerk Wassenaar <tsjerkw at 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 <zjuliuji at 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 <tsjerkw at 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
> >> _______________________________________________
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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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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