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

From: Carlos Simmerling <>
Date: Tue, 22 Oct 2019 17:01:53 -0400

Yes, distance restraints work in pmemd.cuda with nmropt=1. Look in the
manual or search here for "nmr restraints". You can set no penalty below a
certain distance.

On Tue, Oct 22, 2019, 4:12 PM Homeo Morphism <>

> 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.
> Thanks.
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Received on Tue Oct 22 2019 - 14:30:01 PDT
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