[AMBER] Definition of restraints to avoid ligand aggregation

From: Giulio RASTELLI <giulio.rastelli.unimore.it>
Date: Sun, 22 Dec 2019 17:06:16 +0100

Dear All,

I am running a MD simulation (pmemd.CUDA, amber18) of a periodic box system
containing a protein, 500 ligand molecules (all the same) and water.

To avoid ligand aggregation during MD, I would like to define distance
restraints to keep the COM of the 500 ligands away (>5angst) from each
other. Considering that there are 500 ligands in the box, the &rst
definition appears difficult.

Has anybody defined restraints for similar purposes that are easier to

Thanks a lot for the advice.


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Received on Sun Dec 22 2019 - 08:30:02 PST
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