Hi Ji,
The big problem with transition states like these is that you can't
properly describe the tetrahedral intermediate classically; you have
to consider a whole bunch of non-classical interactions with the
environment (the halfway transferred proton from serine to histidine,
for instance). That
Hi all,
It's really a transition state of enzyme catalyzed reaction as Tsjerk said.
Firstly, the hydrogen from serine will bind with the His nearby. Afterwards,
the serine residue will nucleophilicly bind with substrate to form such a
tetrahedral intermediate.
However, i did not attend to explore
Tsjerk Wassenaar wrote:
Hi,
Even worse, this looks like a transition-state product. The hydrogen
originating from the serine will not just have wandered off. It is
unlikely that it happened to go sit on the other oxygen. Rather, the
other oxygen, which would originally be double-bonded would pro
Hi,
Even worse, this looks like a transition-state product. The hydrogen
originating from the serine will not just have wandered off. It is
unlikely that it happened to go sit on the other oxygen. Rather, the
other oxygen, which would originally be double-bonded would probably
form a strong hydrog
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.go
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/Expe
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 contributio
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 appli
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
Hi Mark,
Thank you for your suggestion. As you know, I'm not familiar with the force
field so i can't tell myself which one of the available force field is
suitable to me. Fortunately, I find the force field Gromos96 and Amber have
been adapted in previous studies. So guess i can use these kind of
Ji Liu wrote:
Hello everyone,
I'm gonna run MD simulation with a enzyme/substrate system. Here the
substrate must connected with the side chain of an activity residue of
enzyme through covalent bond. However, i really have no idea about the
preparation of such a complex structure file. Actual
Hello everyone,
I'm gonna run MD simulation with a enzyme/substrate system. Here the
substrate must connected with the side chain of an activity residue of
enzyme through covalent bond. However, i really have no idea about the
preparation of such a complex structure file. Actually, i tried to modi
12 matches
Mail list logo
