Re: [AMBER] Fwd: Domain distances using cpptraj

From: David A Case <>
Date: Sun, 10 Jan 2021 08:23:03 -0500

On Sun, Jan 10, 2021, Athena N wrote:

>I wanted to know if it is possible to find the distances between 2 nuclease
>domains in protein using AMBER.

See the "distance" action in cpptraj. You'll have to decide exactly what
distance you want, e.g. distance between the centers, closest contact
distances, et.

> Also if we have to find the non covalent
>parameters of protein and nucleic acid in a RNP, could we use mmpbsa?

I'm not sure what you mean by the phrase "non covalent parameters".


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Received on Sun Jan 10 2021 - 05:30:04 PST
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