Re: [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA

From: Elvis Martis <>
Date: Fri, 27 Oct 2017 15:06:07 +0000

It would be interesting to try to compute binding energy once including the Mg2+ and once without it. See how the energy values changing or not.
This way you could also validate Miller et al., 2012.

Best Regards
Elvis Martis
Mumbai, INDIA.

From: Alonso Martinez, Diego <>
Sent: 27 October 2017 18:47
Subject: [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA

Dear Amber users,

I’m planning to run MM-PBSA calculations of the binding affinity between a small molecule ligand and a complex formed by a protein, DNA and a Mg2+ ion with All the elements of the complex interact with the small molecule and therefore contribute to the its binding affinity.

When trying to include the metal ion as part of the receptor for the calculation, I read in the Amber manual that “If there is a specific metal ion that you wish to include in the calculation, you can prevent ptraj from stripping this ion by NOT specifying it in strip_mask”.

However, the publication by Miller et al., 2012, mentions that “the implicit solvent models utilized by are not parametrized to account for these species. Therefore, it is not recommended to include water or ions during the calculations”.

I’d like to know if you have previous experience in computing the binding affinity of ligands to metalloprotein + DNA complexes, and if so if you need to add anything into the calculation to adequately parameterize the Mg2+ ion so it is taken into account when calculating the binding affinity. Many thanks for your help.

Best wishes,

Diego Alonso-Martinez
Biomolecular Mass Spectrometry and Computational Proteomics Group (BMSCPG)
Department of Chemical Engineering
Imperial College London (UK)
London SW7 2AZ

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Received on Fri Oct 27 2017 - 08:30:03 PDT
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