Re: [AMBER] MMPBSA Calculation Error: Order of protein and ligand

From: Sundar <>
Date: Tue, 19 Feb 2019 11:35:52 -0600

Can you print your error log here to assess it better?
NATOM mismatch error usually means you didn't prepare your top files
Are you using to prepare the top files?


On Tue, Feb 19, 2019 at 11:23 AM M RCC <> wrote:

> Dear Amber Users,
> I am facing an error in PBSA calculation. and I need a few clarifications.
> My system contains the coordinates of following in the specified order.
> Protein + ligand + cofactor
> MD simulation running well without any error.
> While performing MMPBSA calculation I have prepared the topology as follows
> complex: *Protein + ligand + cofactor *
> receptor: *Protein + ligand + cofactor*
> ligand: *ligand*
> While starting the calculation it gives an error with the complex topology.
> I checked the mdout files. It says NATOM mismatch error. I have comverted
> the prepared topology & crd files of complex and receptor to PBD files and
> it shows the equal number of atoms.
> What am possibly missing here?
> Does it bcoz of the order of the protein and ligand coordinates?
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Sundar Thangapandian
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Received on Tue Feb 19 2019 - 10:00:03 PST
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