Re: [AMBER] Heme parameters

From: Siavoush Dastmalchi <>
Date: Thu, 24 Sep 2020 20:05:29 +0330

Hi Dave,

Sorry that I rushed in sending the previous message. I looked at the mail list and realized that there are quite a few posts. I haven't gone through them yet, but just saw this one, which I guess should be helpful, though haven't checked that out yet.


----- Original Message -----
From: David A Case (
Date: 1399-07-03 18:38
To: AMBER Mailing List (
Subject: Re: [AMBER] Heme parameters

On Wed, Sep 23, 2020, Siavoush Dastmalchi wrote:
>I have problem once again with ligand in my PDB file. It is a heme group.

Antechamber is not set up for ligands that contain metals. Several
people have reported success using Since you just have a
standard heme, there are also a number of published parameter sets: try
a Google search on 'amber heme parameters' for a start.

[It would be great if someone could assemble this information into a
tutorial or something -- heme is a complex ligands, but is a pretty
common one. Collecting what is know in a single place could be a great


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