[AMBER] Make the two ligands independent in one simulation

From: 李明玉 <santaclaus.sjtu.edu.cn>
Date: Fri, 23 Apr 2021 22:18:35 +0800 (CST)

Hi, Amber users

Thanks for your attention!

I would like to study two ligands binding behavior in one protein system simultaneously in a single MD trajectory.

However, the ligands prefer to aggregate together due to the polarity.

I am wondering is there any possible way to make those two ligands independent in a single MD trajectory.
In other words, there is no non-bond energy between the two ligands, so that they can move independently though they are in one protein system!

Many thanks
Pineapple
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Received on Fri Apr 23 2021 - 07:30:02 PDT
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