From: Norman Geist (
Date: Tue Feb 11 2014 - 09:38:29 CST

You could do something like this in the VMD console:


set a [atomselect top "(same residue as (water within 3 of protein)) or

$a writepdb "protein_with_shell.pdb"


You can do the same using File->Save Coordinates with the atomselection text


Norman Geist.


Von: [] Im Auftrag von
surya narayanan chandrasekaran
Gesendet: Dienstag, 11. Februar 2014 13:53
Betreff: vmd-l: reg extracting coordinates for first water shell.



I have a complex surrounded by water and protein. i wanna look at the the
atom interacting with my molecule. I would like to extract the information
of coordinates interacting on the surface of the atom of my molecule. Then i
would like to extract the coordinates for it. for further doing QM/MM
calculation. Any idea in this regard is welcome.

Suryanarayanan C
M.S Chemist