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

From: David A Case <>
Date: Tue, 19 Feb 2019 13:39:34 -0500

On Tue, Feb 19, 2019, M RCC wrote:

>While performing MMPBSA calculation I have prepared the topology as follows

>complex: *Protein + ligand + cofactor *
>receptor: *Protein + ligand + cofactor*
>ligand: *ligand*

Above should not work: loosely, the "complex" should be the combination
of the "receptor" plus the "ligand". Hence, the number of atoms in the
complex should be the sum of the number of atoms in the receptor and the
number of atoms in the ligand.

But in your case, the complex and receptor are identical.


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Received on Tue Feb 19 2019 - 11:00:02 PST
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