Re: [AMBER] parameterization with crystal water

From: David A Case <>
Date: Wed, 25 Mar 2020 21:41:55 -0400

On Wed, Mar 25, 2020, Hira Jabeen wrote:

>I am trying to parameterize protein and ligand complex along with crystal water.

What you want to do is parameterize just the ligand. Use standard Amber
force fields for the protein and the water.

Antechamber is designed to handle single, smallish (MW<1000) organic molecules
only. It will do a terrible job with water, and a bad (perhaps not
"terrible") job with proteins.

...hope this helps....dac

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Received on Wed Mar 25 2020 - 19:00:02 PDT
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