Re: [AMBER] minimization codes

From: Karl N. Kirschner <>
Date: Mon, 22 Jul 2013 10:20:53 +0200 (CEST)

Hello Wang,

  These are atom labels. There will be one unique label per residue and they can be found in the PDB output of leap or ambpdb. GMAX refers to the maximum gradient value of the system (Amber 12 Manual, section 1.4); the atom that has this maximum gradient will be identified under the NAME the atom Number columns. This allows you to identify atoms that are making poor spacial contacts with other atoms, and may need special attention during for proper minimization.

Best regards,

----- Original Message -----
From: "Wang Chern Hoe (Dr)" <>
To: "AMBER Mailing List" <>
Sent: Monday, July 22, 2013 9:00:51 AM
Subject: [AMBER] minimization codes


Does anyone know the meaning of these codes from the output file of energy minimization ? Are they referring to protein atoms or is it the name of an energy minimization algorithm ?


What about GMAX ? What does it mean ? I could not find these in the Amber 12 manual.


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