[gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 29 08:47:03 CEST 2007

Hi Fulya,

I can understand this. But if the person who issued this assignment
thought it was something to do in an afternoon he/she was quite
mistaken. Now, it is still possible to do it, but it depends on how
much time you have. Plenty of people have once started with
parameterization. None of us was born with knowledge of it (as far as
I know). But it does mean that you first have to make sure that you
understand molecular dynamics. You have to understand the (role of)
the force field and the philosophies behind force fields. You'll have
to choose a force field which you think fits best with what you want
to do. Then you'll have to get to understand the conditions for that
particular force field; usually there is a strict interplay between a
force field and simulation parameters, notably the treatment of
electrostatic interactions, the cut-off range and the water model.
You'll have to find a study describing the parameterization of a
molecule for that force field and replicate it, to see if you can
reproduce the results and then you're probably ready to try to tackle
your molecule.

Now, sulfite bound tyrosine is not merely a coupling between a
well-parameterized tyrosine residue and a well-parameterized sulfite
group. Tyrosine and sulfite are both conjugated systems, which is well
fun if you bind them together. That will change the whole charge
distribution on both.

That being said.., have you already checked for a description of
sulfite tyrosine in the literature? That would save you a good deal of
trouble. Otherwise you'll have to convince your supervisor to allow
you more time.

Good luck,


On 3/29/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> fulya caglar wrote:
> > Hi Tsjerk,
> > Thanks for your help.You're right about "taking paths well walked by
> > others,before starting new trails" but I have to do this simulation for
> > my study:(
> If whoever set this problem didn't understand this problem with sulfite
> parameters, then they've set a poor problem for a person new to MD. That
> implies a poor knowledge of MD and of people. Perhaps you should
> renegotiate your problem, or choose a new setter :-)
> Mark
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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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