Hi Rahul,
Try the following mask
":799 <.8.0 & !.H="
This will include all atoms within 8 A of residue 799 (i.e your ligand) and
exclude H atoms.
You don't need to explicitly mention ions and water if you don't want to include
them.
Hope it helps,
Senthil
________________________________
From: Rahul Banerjee <rahul.banerjee.chemistry.msu.edu>
To: "amber.ambermd.org" <amber.ambermd.org>
Sent: Wed, September 8, 2010 10:27:42 PM
Subject: [AMBER] Atom selection
Dear All,
I want to calculate RMSD for all protein heavy atoms (back bone and sidechain,
without H) within 8.0 A of my ligang (resid 799) molecule. Also there are waters
and ions (Na+) in my system which needs to excluded for this calculations. The
following rms comand doesn't work:
rms first out output.rms :799<.8.0&!.H=&!.Na+&!:WAT time 10
Can you please tell me how it might work?
Rahul
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Received on Fri Sep 10 2010 - 07:00:03 PDT
