Hi David, thanks for the reply. Let me clarify a little, I am referring to the dinucleotide as the "ligand" in keeping with the convention used by the force-field converter.
I used cgenff to generate the initial CHARMM parameters and run in NAMD. In the force-field converter it asks what force field you want to use for each type of molecule in your system (RNA, protein, ligands, etc.). For "ligands" (which in my case included only the dinucleotide in question), I chose GAFF2, but another option is OpenFF. I'm wondering if perhaps OpenFF will be more appropriate for this molecule.
I looked at RMSD of both the dinucleotide and of the surrounding RNA, and both looked pretty good with no unreasonable increases.
Collin
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Monday, September 26, 2022 8:45 AM
To: Collin Nisler <cnisler.uchicago.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Using CHARMM-GUI FF Convert from CHARMM to Amber With Ligand
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
>cgenff?
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?
....dac
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Received on Mon Sep 26 2022 - 08:00:03 PDT
