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

[Tsjerk Wassenaar]

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