Re: claen water

From: Nicholas M Glykos (
Date: Mon Aug 30 2010 - 08:26:44 CDT

Hi Axel,

> > Still, if there time for just one simulation, I would rather remove any
> > waters 'trapped' in buried protein cavities.
> you say, that 'disordered waters' will most likely
> not show up in x-ray. ok, but how does this justify
> removing water that _does_ show up in the PDB file?

Ah, I think I can see the reason for the misunderstanding. I should have
specified that I was referring to waters 'trapped' in a cavity by the
solvation step (during system preparation), and, of course, not for
crystallographically determined waters. I thought that explicitly
referring to simulation and quoting 'trapped' would have made that clear,
but obviously it didn't.

> that being said, if water is trapped due to unphysical
> processes, e.g, assembly of a system through a VMD
> script, then indeed, it is justified to remove those. yet,
> overall people seem to have an idealized picture of
> how "pure" phases in systems are. most are pretty
> "dirty" in real life. we tend to idealize, because that makes
> setup, equilibration, and simulation much easier.

Still, most people would be sceptical with the presence (in an MD system)
of a couple of water molecules buried deep in the middle of protein's
hydrophobic core [and they would possibly argue that in order to place the
waters there you do need some evidence for their presence (and not absence
of evidence for their absence)].

For the example quoted in the previous example (>200 cubic Angstrom
cavity), the un-physical (to my mind) would be to have a such a large
volume of completely empty space buried in the middle of a protein. But
for those frequent smaller cavities ? And for those smaller cavities that
never ended-up with a water inside just because the file wat.pdb didn't
have a water at the 'right' coordinates ? In other words, I would
completely agree with you that "there is no Royal road to system
preparation" :-)


          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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