VMD-L Mailing List

From: siddesh southekal (siddeshonline_at_gmail.com)
Date: Fri Dec 17 2010 - 07:18:17 CST

Dear all,

I have a pdb file (after 20 ns MD run ) with a membrane protein (GPCR)
embeded in the lipid bilayer with buffer around .There is excess of water
molecules in this file . I want to remove this excess buffer such that i
have water molecules only 10 A above and below the protein .(say around 15 A
around the lipid ) .The membrane normal is in y direction.
I would be using the truncated file for MD simulation using AMBER.
I tried -
set selwater [atomselect top "name OH2 and not within 10 of protein "]
But whn i try to save the selection the pdb file is blank.How do i exactly
do this?
I would appreciate any suggestions
Thanks ,
Siddesh
Universitaet Bonn