Re: claen water

From: Axel Kohlmeyer (
Date: Mon Aug 30 2010 - 07:53:17 CDT

On Mon, Aug 30, 2010 at 5:22 AM, Nicholas M Glykos <> wrote:
>> is it necessary to clean water in between the protein? I understand we need
>> to clean in channels or pores but is it required for globular proteins?
> There is an interesting point to your question. Are (relatively large)
> protein cavities empty or not ? If they contain (structurally disordered)
> water molecules, then these waters will most probably not be visible in
> electron density maps (and there will be no evidence for their presence
> from the deposited PDB file). Last time (centuries ago) that we had this
> issue (with a buried cavity of no less than 270 A^3 !), we ended-up doing
> simulations both with and without waters in the cavity (not that this
> ideal, the number of water molecules placed in the cavity will matter).
> Still, if there time for just one simulation, I would rather remove any
> waters 'trapped' in buried protein cavities.

hmmm... i cannot quite follow your argument.
please correct me, if my assessment is wrong.

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?
those are most likely strongly bound, or else they
would not show up, and might even be instrumental
in stabilizing the given structure.

i would also say, that any cavity would be filled
(but how much?) with something, rather than nothing,
unless there is a mechanism, that can remove those
molecules faster than they can enter.

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.

> My twocents,

i'll see your two cents, and raise by another two,

> Nicholas
> --
>          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,

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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