[gmx-users] Bulk waters placed inside protein core

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Fri Oct 15 12:07:13 CEST 2004

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.


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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list