Re: [AMBER] NMR refinement of G-Quadruplex DNA by AMBER22

From: David A Case via AMBER <>
Date: Mon, 13 Feb 2023 08:20:07 -0500

On Sun, Feb 12, 2023, Anirban Ghosh via AMBER wrote:
>I am using AMBER22 to calculate the NMR conformation of the G-quadruplex
>using restraints for the 1st time.

>However, it is not clear to me where to modify to calculate the 100
>conformations and select the best 10/20 best on final energies. Please help
>me to change the script.

Best thing (currently) is to use the imin=5 option in sander to carry out a
single point calculation on each of the snapshots in your trajectory file.
You can then then choose which ones are the "best" based on some combination
of energy and NMR restraint.

...good luck....dac

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Received on Mon Feb 13 2023 - 05:30:02 PST
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