AMBER Archive (2009)

Subject: [AMBER] restraining atoms

From: neville forlemu (
Date: Thu Jan 22 2009 - 08:53:48 CST

I have a quick question about restraining atoms, during a minimization or md run using amber.
Lets say you have a homotetramer (subunits A,B,C,D).
In the pdb file each subunit the residues are number as follows
A1-A300, B1-B300 etc

a minimization, where I intend to only minimize the salts and water can
I restrain all the residues in the protein by specifying

res 1 1200

or should I differentiate the subunits like

res A1-A300 etc.


--- On Thu, 1/22/09, Lake, Thomas <> wrote:
From: Lake, Thomas <>
Subject: [AMBER] (no subject)
Date: Thursday, January 22, 2009, 7:43 AM

I am trying to generate an average PDB structure, from a PDB containing
multiple structures. I think I need to use ptraj to do this, but am not
sure what to write in the input file. Can anyone help.


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