[gmx-users] Bulk waters placed inside protein core

[Choon Peng]

Hi David,

  Oh, we happen to come across this program today!
Will check that out.
Thanks.

regards,
choon peng

On Fri, 15 Oct 2004, David van der Spoel wrote:

> On Fri, 2004-10-15 at 12:07, Daan van Aalten wrote:
> > Hi Choon Peng
> >
> > This looks OK to me - because what is the alternative - to leave a big
> > gaping hydrophilic hole in your apolar core?
> > Although you don;t mention it, it is possible that before placing
> > bulk water you have deleted the crystallographic waters (if your starting
> > structure is a crystal structure, that is) - this is considered bad
> > practice. There are many examples of "structural" waters in protein cores
> > that are important for proper packing - at the very least these (but in
> > general any water with a least 2 H-bonds to the protein, in my opinion)
> > should be left in place when you are adding bulk solvent.
> >
> To test good positions for waters (i.e. to test whether there should be
> a water in your protein core) you could try to run the DOWSER program by
> the Jan Hermans group.
>
> > Daan
> >
> > On Fri, 15 Oct 2004, Choon Peng wrote:
> >
> > > Dear all,
> > >
> > >    I'm interested to look at water exchange events of proteins, where bulk
> > > waters may penetrate into the interior of a protein.
> > > So, accurate bulk water placement is very important.
> > > But both my GROMOS96 and OPLS-AA simulations show one to several bulk water
> > > molecules being placed next to a polar residue in the core of protein by
> > > genbox.
> > > Probably not many people noticed this because most people do not need to
> > > visualize where the bulk waters are. My guess...
> > >
> > > I would like to know if this is a bug in the code?
> > > Or an 'artifact' due to the presence of a polar group in the hydrophobic
> > > core of the protein?
> > > The PDB protein structure I'm using is a mutant where the deepest buried
> > > residue is mutated from a hydrophobic to a hydrophilic one.
> > >
> > > I'm using GROMACS-3.2.1.
> > >
> > > Thank you.
> > >
> > > Regards,
> > > Choon-Peng CHNG
> > >
> > > --
> > > Mr Choon-Peng CHNG
> > > Research Associate
> > > Computational Biology Group
> > > Bioinformatics Institute, A*STAR
> > > 30 Biopolis Street, Level 7. Singapore 138671.
> > > DID: +65 6478 8301 FAX: +65 6478 9047
> > > WWW: http://www.bii.a-star.edu.sg/~cpchng
> > >
> > >
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> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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