Re: [AMBER] Charged species with antechamber

From: David A Case <>
Date: Sat, 12 Dec 2020 21:39:12 -0500

On Thu, Dec 10, 2020, Sam Walsworth (Researcher) wrote:
>The charged species I'm working with is pyruvate which is coupled with
>NADH co-factor (PYR-NADH) to form a ligand for use in a simulation
>binding to Lactate Dehydrogenase A (LDHA:PYR-NADH)

I guess I'm confused here: you say above that pyruvate is "coupled" with

>Would it be worth treating PYR-NADH as one species? I was planning
>on using antechamber for pyruvate on its own since amber ff99SB has
>residues for NADH (thank you Ross Walker) and also since they aren't
>covalently bonded to each other,

...but here you seem to say that the two are not covalently bonded.

Antechamber should deal with single, complete molecules. I'm not sure
what you have here as your "ligand".


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Received on Sat Dec 12 2020 - 19:00:02 PST
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