[gmx-users] Bulk waters placed inside protein core
cpchng at bii.a-star.edu.sg
Fri Oct 15 16:05:20 CEST 2004
Thank you for the reply.
Sorry, I forgot to mention that I've kept the crystal waters.
I used to delete them with I first started doing MD but later realized
Actually, we wish to investigate whether the buried waters escape from the
protein and whether bulk waters enter the protein.
So, it is important for accurate placement of bulk waters before
>From what I can understand, genbox removes water molecules that overlap
with protein atoms. So, for a protein with a large hydrophobic cavity,
will added water molecules remain undeleted and expected to escape with
On Fri, 15 Oct 2004, 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.
> 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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