AMBER Archive (2002)

Subject: SUMMARY: solvating a protein with large cavity

From: Tom Bishop (bishop_at_tulane.edu)
Date: Wed Dec 18 2002 - 09:03:27 CST

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 

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