Re: [AMBER] Using CHARMM-GUI FF Convert from CHARMM to Amber With Ligand

From: David A Case via AMBER <>
Date: Mon, 26 Sep 2022 08:45:51 -0400

On Sun, Sep 25, 2022, Collin Nisler via AMBER wrote:

>I used the Force Field Converter on the
>CHARMM-GUI website to convert an RNA system from CHARMM to Amber, with the
>goal of running the simulation in NAMD using the OL3 force field for the
>RNA. The system also contains a dinucleotide with a non-canonical backbone,
>which was parametrized using the cgenff server.
>I used the GAFF2 force field for the ligand, but was thinking perhaps
>I should try the OpenFF force field input option. Is one or the other
>of these options recommended given the ligand force field came from

I'm a little lost here: Is the dinucleotide the "ligand" here?

In the top paragraph, you say that you used cgenff for the ligand, but in
the second paragraph you say you used GAFF2 for the ligand. Can you clarify
what is going on?

My take, based on incomplete information: if the force field for the ligand
changed, it is not surprising that you might see a conformational change
there. If the ligand force field has not changed, look at the RNA
surroundings (that are in contact with the ligand): has there been any
conformational change there, as one might expect in going from the CHARMM
RNA parameters to the Amber one?


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Received on Mon Sep 26 2022 - 06:00:03 PDT
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