[AMBER] Physical chemistry question regarding entropy calculations in ligand-receptor system

From: Liao <liaojunzhuo.aliyun.com>
Date: Wed, 28 Jul 2021 14:33:34 -0500

Dear Amber community experts,

We probably all know about the costliness of running entropy calculations in a large protein-ligand system. There were methods of pruning the protein and retaining the binding pocket region only to speed up the calculation reported in the years around 2012 or earlier. It works well since one only needs a delta S.

Now I wonder, let’s say with a completely rigid receptor, if we want to compare the entropy difference of 2 poses of the same ligand, or entropy difference of 2 ligands, couldn’t we just remove the receptor completely and use the S value from the standalone ligands/poses only? Binding enthalpy can be calculated separately with the receptor present very quickly with MM/GBSA.

I mean docking actually uses completely rigid receptors in a lot of the cases from my knowledge.

Thanks there.

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Received on Wed Jul 28 2021 - 13:00:02 PDT
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