[AMBER] one question about setting up amber simulation on negatively charged ligand

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From: laura zhang via AMBER <amber.ambermd.org>
Date: Fri, 2 Dec 2022 20:34:33 +0000

Dear all,

I tried to set up a simulation including a protein and two small ligands. One ligand is negatively charged (charge density -1). when I added H to this ligand and also tried to neutralize it in Chimera, Chimera showed error. So, I only added H to this ligand using Chimera, and kept its charge as -1. Then, when I ran antechamber to prepare the mol2 and frcmod files for this ligand, antechamber crashed because of its charge.

I am wondering how to solve such kind of issue. Thank you very much.

Laura

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Received on Fri Dec 02 2022 - 13:00:02 PST