[gmx-users] Bulk waters placed inside protein core
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 15 13:31:14 CEST 2004
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.
> 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 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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