Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center

Date: Wed, 24 Feb 2021 10:50:23 +0530


I have gone through the binding_energy.mmpbsa input carefully and have seen
that there are two options under radiopt (I used 0 which is used by default
for using the radii from the prmtop file). So as per my understanding, the
input should read all the radii provided by the prmtop. I am adding the
error message here:
*No radius found for ZN 9577 in residue ZN1 595*

I have used for the modeling of the system. Thus, It named the zinc
coordinated ligands differently (like HE2, AP1, WT1 or ZN1). But all the
parameters read from the prmtop file by checking the type only, right? Or
does this naming system itself creates a problem here?

Thanks in advance,
Satyajit Khatua

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Date: Sun, Feb 21, 2021 at 1:30 AM
Subject: AMBER Digest, Vol 3280, Issue 1
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Message: 5
Date: Sat, 20 Feb 2021 09:24:25 -0500
From: David A Case <>
Subject: Re: [AMBER] Interaction energy by MM-PBSA for a superantigen
        with important Zn(II) center
To: AMBER Mailing List <>
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On Fri, Feb 19, 2021, SATYAJIT KHATUA wrote:
>I am calculating the protein-protein interaction energy for a superantigen
>system. I am using MM-PBSA for that estimation. But, the problem is that I
>have an important ZN (II) center through which the two fragment interacts.

If the zinc bridges the two proteins, you essentially have a covalent
connection, and it will be hard to get binding energies. Think carefully
about what reactions you are studying, what experimental data you might
have, and what you would do with the result.

>When I have subjected the trajectory to binding energy estimation, it
>couldn't able to detect the radius for the metal center.

Look at at the "radiopt" option, which will use the radii in the prmtop

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Received on Tue Feb 23 2021 - 21:30:02 PST
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