Re: [AMBER] DNA protein simulation protocol

From: David A Case <>
Date: Mon, 25 Jan 2021 22:11:46 -0500

On Mon, Jan 25, 2021, Airy Sanjeev wrote:

>I am trying to perform a DNA-protein simulation but found the error
>Info: The number of bonds (512) exceeded MAXBOND.
>Total number of electrons: 7208; net charge: 0
>I am trying for antechamber, please guide me what are the protocols to be
>followed for performing a DNA-protein complex.

You don't say what program gave the error you report, but it looks like
antechamber. Antechamber is designed to look at small, drug-like organic
molecules, or *single residues*. It would never work for a system with
7000 electrons.

A protein-DNA simulation is not really any different than a protein-only
or a DNA-only simulation. See tutorials 5.2 or 5.4 for basic examples of
biomolecular simulations.

...hope this helps...dac

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Received on Mon Jan 25 2021 - 19:30:02 PST
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