AMBER Archive (2002)

Subject: Re: SUMMARY: solvating a protein with large cavity

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Dec 18 2002 - 19:21:23 CST

Hi,

Sorry to interfere in the discussion I was wondering if there is a special
procedure to solvate a protein channel (pore)? The issues below apply in
this case too? (Diameters ranging from 16A to 30A).

Thanks,
Ioana

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On Wed, 18 Dec 2002, Tom Bishop wrote:

> For anyone that was following this thread.
> Here's what we came up with.
>
> In general the "Leap" solvate commands work well for bulk solvent, but
> do not expect these commands to place ANY waters specifically. The
> equilibration phase will
> locate waters specifically if the location is accessible, but cavities
> should be addressed
> on an individual basis, even for very large cavities.
>
> Good luck,
> TOm Bishop
>
>
> On Mon, Dec 16, 2002, Thomas wrote:
> >
> > Here's what I finally worked out to get the waters put in, where
> > {27.7 25.9 35.4} is the center of the cavity
> >
> > solvatecap REC WATBOX216 { 27.7 25.9 35.4 } 12 .75
> >
> > solvatebox REC WATBOX216 6
> >
>
> Sounds good. I have never used the solvateCap or solvateShell commands
> myself, so I can't help out very much.
> >
> >
> > In general if there are small cavities in a protein would it make sense
> > to solvate it in two stages. Stage one try to gets waters in the
> > cavities with a reducued closeness
> > parameters and then stage 2 add bulk waters.
> >
>
> Stage 1 might require some different program. Take a look at:
>
> http://www.bch.msu.edu/labs/kuhn/web/software.html
>
> A google search on "protein solvation sites" turns up a number of
> promising
> hits (including the one above). You might also ask on CCL how others
> get
> starting positions for waters in cavities.
>
> ..good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>