[gmx-users] compare simulations between wt and mutate protein

[Tsjerk Wassenaar]

Hi Andrea,

I think it's a good thing to start another simulation by mutating the
wt at 20ns. Besides, it would be good to mutate the mutant at 20ns back, to
see if it goes the other way. In any case, you'll have to perform
multiple simulations. For a strategy on comparing simulations, to see
which properties are affected, you can have a look at chapters 2 and 4
of my thesis, which I know you have. Comparing with respect to the
"internal dynamics" by means of PCA is also a good possibility and
would generally be approached by "Combined Essential Dynamics", but I
would note there are better methods.

Best,

Tsjerk

On 4/3/07, Pedro Alexandre de Araújo Gomes Lapido Loureiro
<palaplou at gmail.com> wrote:
> Hi Andrea,
>
> I think two 20 ns simulations of wild- and mutated protein won't *guarantee*
> that your results are significant, but, of course, they can be!
> MD suffers from sensitivity to initial conditions, that gets worse with
> "short" simulations, as you know.
>
> I think you have to have an idea of the relaxation time of the process you
> are interested in.
> One thing is to study side-chain isomerizations, another is motions
> involving the protein backbone.
>
> PCA is related to the covariance matrix of atom coordinates and can also be
> used in the dihedral space.
> Check the papers on  the cosine content of principal components, for
> instance. They can give you an idea of the "extent" of your simulation...
>
> Regards.
>
> Pedro.
>
>
> 2007/4/2, spitaleri.andrea at hsr.it <spitaleri.andrea at hsr.it>:
> >
> > Hi all,
> > I am performing a MD study using as starting point a protein whose
> > structure has been determined by nmr. the md of wild type has show few
> > structural changes of some sidechains after 20ns. Afterfwards, using the
> > same starting point but mutating a PRO to LEU, I have perfomed a similar
> > MD. The structural behaviour of the mutate protein is a bit different
> > (fair enough) from the wt. However, I was wondering whether it should be
> > more fair perform a MD for the mutate protein using the as starting
> > point the equilibrated structure (after 20ns) of the wt.
> > Second, performing different MD on the wt and the mutate protein, how
> > may compare properly the results (a part of rmsd, energies, sas, hbond,
> > etc..)? Is it logic to perform a PCA on the energies values? Any
> > suggestion are welcome.
> >
> > Thanks in advance
> >
> > Regards
> >
> > andrea
> >
> > Andrea Spitaleri PhD
> > Dulbecco Telethon Institute
> > c/o DIBIT Scientific Institute
> > Biomolecular NMR, 1B4
> > Via Olgettina 58
> > 20132 Milano (Italy)
> >
> >
> >
> >
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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