[AMBER] constraining ligands to some distance from a target molecule on pmemd.cuda

From: Homeo Morphism <homeo.morphizm.gmail.com>
Date: Tue, 22 Oct 2019 23:11:36 +0300

I'm trying to obtain a trajectory of a ligand binding to a certain GPCR. To
that end, I position roughly 10 equivalent ligands at some distance from
receptor's extracellular loops and then use charmm-gui for insertion into
the membrane, solvation, etc.

There's always a ligand that tries to escape the periodic box through its
upper edge and thus end up in the lower parts of the box - interacting with
intracellular loops of the receptor. I'd want to avoid that.

Is there any way I can stop the ligand from doing that? In NAMD I did that
by introducing by means of scripting a weak artificial force that pushed a
ligand toward ECLs whenever it was not within, say, 20A of ECLs. Is there
anything like that in Amber?

I've looked through Amber manual and found description of constraints and
restraints, but if I'm not mistaken they seem to work only in sander, and I
need an approach for pmemd.cuda-version.

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Received on Tue Oct 22 2019 - 13:30:02 PDT
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