VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Aug 31 2007 - 08:16:08 CDT

Hi Shulin,
the solvate in the vmd console should give you a water box; the best way
to get a sphere is just to make a box with solvate, and then cut out
your protein enclosed in a sphere. You can do this either by:

Making a selection (eg, "not (same residue as x*x + y*y + z*z > 2500)"),
saving a pdb, and then running it through psfgen to make a new psf/pdb combo

or

Using psfgen directly. Read the psf and pdb with the water cube, and
have psfgen delete everything that you don't want.
eg.
package require psfgen
readpsf solvate.psf
coordpdb solvate.pdb
mol new solvate.pdb
set badsel [atomselect top "oxygen and water and same residue as x*x +
y*y + z*z > 2500"]
foreach segn [$badsel get segname] resid [$badsel get resid] {
    delatom $segn $resid
}
writepsf solvate-sphere.psf
writepdb solvate-sphere.pdb

Best,
Peter

Shulin Zhuang wrote:
> Dear All
>
> I want to solvate my protein in a water sphere with a radius of 50
> angstram, but when I use the solvate tcl in VMD TCL console, I could
> not do it. Does anyone has the script to solvate proteins in large
> water sphere? If does, wish you will share it with me. Great thanks!!!
>
>
> Best regards
> Shulin