[gmx-users] Re: Select atoms in a residue

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Tue Sep 3 17:36:35 CEST 2013

Hello Justin, 

My question was  "How to select the following atoms CG, CD1, HD1, CD2, CE3, HE3, CZ3, HZ3, CH2, etc.. present "ONLY" in the trp residue with a single line command with make_ndx. Indeed some of them can be also present in other residues. 



Message: 4
Date: Tue, 3 Sep 2013 12:57:25 +0000
From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
Subject: [gmx-users] Select atoms in a residue
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
        <3E39B768BB199548AB18F7289E7534AF1A880C06 at EXDAG0-B0.intra.cea.fr>
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Hello all,

A Quick question below:

My peptide contains one trp, and i want to select only the atoms that form the the indol ring. I would like a portable script for others systems that contain also a peptide with one Trp residue. So I am not interesting to select the corresponding atoms by their numbers in the pdb/gro files

The atom name in the indol group are  aCG | aCD1 | aHD1 | aCD2 | aCE3 | aHE3 | aCZ3 | aHZ3 | aCH2 | aHH2 | aCZ2 | aHZ2 | aCE2 | aNE1 | aHE1

Can you help me ?



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