Re: [AMBER] How to set a replusive force between two drug molecules or two atoms.

From: Pengfei Li <>
Date: Mon, 6 Sep 2021 18:14:05 -0500

Hi Ning,

If you are using AMBER, maybe you can consider to slightly change the Lennard-Jones parameters between these molecules or add some weak NMR restraints between these molecules. ParmEd may help you to solve your problem (e.g. changeLJPair and changeLJSingleType commands in ParmEd, note that these two commands are for atom types).


> On Aug 7, 2021, at 10:28 PM, wrote:
> Dear, Amber experts.
> In my researches, some weak replusive force between molecules may need to be setted to prevent the unexpected aggregation where these molecules surround the possible target protein in the solvent system. But I don't know how to set this parameter. Please help me. Any suggestion is welcome.
> Best regards.
> --------------------------------
> Ning Wang <PhD>
> National Laboratory of Biomacromolecules
> Institute of Biophysics, Chinese Academy of Sciences
> My reseached interests has foucsed on protein structure determinated by Cryo-EM, virtual screening of potential drugs, protein molecular dynamic simulation, and protein design via computational biology.
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Received on Mon Sep 06 2021 - 16:30:02 PDT
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