[gmx-users] Bulk waters placed inside protein core

[Choon Peng]

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