Thank you very much for helping. After using "-nc -1" in the antechamber command line, it worked!
Laura
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Friday, December 2, 2022 16:45
To: laura zhang <lqzhang0332.hotmail.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] one question about setting up amber simulation on negatively charged ligand
On Fri, Dec 02, 2022, laura zhang via AMBER wrote:
>
>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.
You don't say what you mean by "antechamber crashed". If the ligand has a -1
charge, you need to add the "-nc -1" flag to your antechamber run.
If that is not the problem, we would need more info about what you tried, and
exactly what the error message was.
....regards...dac
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Received on Fri Dec 02 2022 - 18:00:02 PST
