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

[Ji Liu]

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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