[AMBER] How to restrain minimum distance between proteins?

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Tue, 25 Oct 2022 00:11:15 -0400

Dear AMBER community,

I’m running simulations where there are two proteins in the simulation box and I need to prevent them from getting close enough to interact. Is there a way to restrain the minimum distance between any pair of atoms for the two proteins?

I’ve tried all sorts of restraints (e.g., fixing the X-, Y-, and Z-components of the centers of mass), but somehow the minimum distance always gets smaller.

Best,
Matthew


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Received on Mon Oct 24 2022 - 21:30:03 PDT
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