Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Fri Mar 16 2007 - 12:55:34 CDT

Hi Won-Young,
By typing "solvate" in the TkCon (Extensions > Tk Console), you will
see all the options which you can specify for the solvate package.
Of particular interest to you might be the -b option which defines
the minimum distance between water and solute molecule(s). Default
is 2.4 A, so reducing this number may allow for waters to be placed
in the small "hollow spaces" you talk about. If that doesn't work,
you may also try to place water molecules by hand (perhaps by moving
some bulk solvent waters using VMD's move command). You may also be
interested in the DOWSER program, which surveys molecules the asses
the hydrophobic/hydrophilic nature of their cavities, etc.
http://hekto.med.unc.edu:8080/HERMANS/software/DOWSER/
-Tim

On Mar 14, 2007, at 2:46 PM, <wahn_at_uiuc.edu> <wahn_at_uiuc.edu> wrote:

> Dear NAMD users,
>
> How do you solvate your protein or whatever the molecule?
>
> I have used the solvation function of VMD.
> But, my system after solvation does not have enough water molecules
> and contains a kind of hollow space in it.
>
> How may I adjust and measure the water density of my system?
>
> Your comment could save me a lot of time and efforts.
> Thank you.
>
> Won-Young
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