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I have been looking all over the internet for forcefield parameters for a fluorescent probe called NBD (nitrobenzoxadiazole). Here is an example of an NBD labeled fatty.

I have so far only found parameters for AMBER or GROMACS. Also when following the articles from these two reviews, there seem to be no CHARMM parameters anywhere.

My questions are:

  • What CHARMM forcefield parameters would you use for NBD?
  • How could I transfer the AMBER or GROMACS parameters for use in CHARMM?
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1 Answer 1

Converting between force fields is always an iffy affair, as different force fields were parametrized with different reference sets, and possibly even with different intent in mind.

You have two options here:

  1. You can extract the raw parameters from the particular GROMACS or AMBER force field used here, and try to translate them into the parameter formalism CHARMM uses. Generally speaking, force fields consist of a set of parameters for each atom type, and a set of equations these parameters are used in to calculate forces and geometries. Those equations represent aspects of the atom's or molecule's properties that have an influence on the calculated forces or the molecule geometry, like bonding interactions, non-bonding interactions, angle contraints, bond length constraints, and so on. You need to find the corresponding equations in CHARMM's force field framework, and then translate the parameters from AMBER or GROMACS so that the force field is the same in CHARMM.

  2. Alternatively, you can look at the various CHARMM force fields and try to find one that works with NBD and any other molecules you got in your simulation. The first article you cited details where the various general parameters they used were from and how their simulation in GROMACS was set up. You should be able to define the same simulation parameters in CHARMM and rerun their simulation there. You can then use their published data to benchark your own simulation against theirs.

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