Re: [AMBER] FW: Building topology of a molecule with Antechamber

From: David A Case <>
Date: Wed, 6 Feb 2019 07:56:02 -0500

On Wed, Feb 06, 2019, fateme haghighi wrote:
>I am trying to build topology of a molecule by Antechamber.

> After docking I used the output file of ligand for building topology by
>amber99SB force field but I have received number of errors about angel
>and so on. In addition, the output topology file has not any mass and

Can you say *exactly* what you did here? You mentioned using Antechamber,
but that program doesn't create topology files. I'm guessing (very much
a guess) that you might have run antechamber asking for "Amber atom
types", then somehow fed those files into tleap. That would likely lead
to "errors about angle", but those errors would have prevented tleap from
creating a prmtop file.

I recognize that it can be easy to make mistakes in creating Amber
libraries for molecules. But we can't help without detailed information
about the steps you took. Please also give the exact wording of any
error messages you receive.


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Received on Wed Feb 06 2019 - 05:00:02 PST
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