Re: solvating a protein

From: Giovanni Bellesia (
Date: Thu Jul 13 2006 - 11:54:36 CDT

one easy procedure to solvate a protein could be:
1) open vmd
3) open the Tk console (from the menu "Extensions")
4) cd to the directory in which your psf pdb files are
5) type in "package require solvate" and then type "enter"
6) now a simple example ... type in:
solvate filename.psf filename.pdb -t 10 -o filename-wbox
and then "enter".

This should create two files: filename-wbox.psf and filename-wbox.pdb
which contain all the information for 'your' solvated system.
In more details the option -t 10 builds a water box in which there is a
10 Angs.
water layer surrounding your protein (in x,y,z directions).
Type in "solvate" and then "enter" if you want to see all the options of
the solvate command.

Hope this will help


>This may be a trivial question. To solvate a protein, the tutorial says one needs to alreayd have a
>pdb and psf files of a water box alone. How does one create a water box alone?
>Thank you,

Giovanni Bellesia
Department of Chemistry & Biochemistry
University of California, Santa Barbara
Santa Barbara, California 93106-9510, USA.

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