VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
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
protein"]

$a writepdb "protein_with_shell.pdb"

 

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

 

Norman Geist.

 

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

 

hi,

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
01742857830