Re: [AMBER] System preparation for

From: David A Case <>
Date: Wed, 4 Nov 2020 08:09:15 -0500

On Wed, Nov 04, 2020, SATYAJIT KHATUA wrote:
>I am talking about the systems where Zn is pre-coordinated to one of the
>protein systems (so, P-Zn + P -> complex case).
>In one system, the water ligand bound to the zinc ion is not quite replaced
>by some atom of a protein. From literature what we know is there are three
>amino acids bound to zinc (two from the zinc bound protein (P-Zn) and one
>from the other protein (P)) in the complex. They also pointed out that the
>fourth coordination position on zinc may be occupied by a water molecule as
>they didn't observe any water signature near zinc in the electron density
>For the second case, the coordination number on zinc is satisfied by four
>amino acid residues (three from P-Zn and one from P). I think this is the
>case that you have mentioned in your third point.
>Can you guide me on how should I proceed further?

Sounds like you could just try treating P-Zn as the "receptor" and P as
the "ligand". (Or the reverse: the names "receptor" and "ligand" are just
tags, and you could equally well call the two moieties that are forming
the complex "A" and "B".)

I'm still concerned that PB/GB results for divalent ions depend very
stronly on the dielectric radii that are used. Be sure you will get more
out of the calculation than just one number (the free energy of complex
formation), since that number is likely to have a large uncertainty.


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Received on Wed Nov 04 2020 - 05:30:03 PST
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