[AMBER] making a box with restraints so ligand does not float away

From: ranjit pillai <rapidrandomreponseunit.gmail.com>
Date: Sun, 17 Nov 2013 19:55:08 +0000

Greetings all,

I am trying to make a box around a protein and ligand in explicit solvent,
so that binding events can be captured as shown in this paper:


The paper uses flat bottomed harmonic restraints to make the box and
prevent the ligand from floating away from the protein. I read advanced
tutorial 4 on distance restraints, but don't think this is going to help
make the box.

I'm a bit overwhelmed by the restraint section in the manual and was hoping
someone knew a good method for creating the box that could be used with the
GPU code in amber 12?

Warm regards,
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Received on Sun Nov 17 2013 - 12:00:03 PST
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