Hello
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)
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, I imagine this would cause issues with antechamber? The paper I'm reproducing manually applied parameters from the R.E.D. Database Project but I decided antechamber would be a better method for parameterising my ligand.
Thanks in advance
Sam
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 10 December 2020 18:00
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Charged species with antechamber
On Thu, Dec 10, 2020, Sam Walsworth (Researcher) wrote:
>
>I am aware that you can use antechamber to parameterise charged molecules
>(using the -nc flag) but I was considering if this is a reliable/tested
>method? I'm currently going through tLEaP and received an error saying
>'The unperturbed charge of the unit (1.001001)
Antechamber can yield charges that don't exactly add up to 1 because of
rounding. You can subtract 0.001 from some atom in the molecule to get
an exact integer.
....dac
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Received on Thu Dec 10 2020 - 11:30:03 PST
