[AMBER] Fast ibelly?

From: David Minh <daveminh.gmail.com>
Date: Tue, 20 Mar 2012 11:29:00 -0400

Hi AMBER developers,

Would it be difficult to make "belly-type" dynamics fast? I'd like to see whether using AMBER with a fixed protein and flexible ligand can do molecular docking well. (As I understand it, the current use of AMBER with DOCK is as a postprocessing step in which all the molecules are able to move, even if there are harmonic restraints, and this isn't faster than a normal AMBER run.)

Also, why is ibelly unavailable with igb>0?


"Flag for belly type dynamics. If set to 1, a subset of the atoms in the system will be allowed to move, and the coordinates of the rest will be frozen. The moving atoms are specified bellymask. This option is not available when igb>0. Note also that this option does not provide any significant speed advantage, and is maintained primarily for backwards compatibility with older version of Amber. Most applica- tions should use the ntr variable instead to restrain parts of the system to stay close to some initial configuration. Default = 0."
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Received on Tue Mar 20 2012 - 08:30:02 PDT
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