Wonderful, thank you! This example file and your description should be sufficient to get me going, and if it gets tricky I will ask on the gromacs email list. I'll share the resulting XML file when I have a working solution.

Just one more question: when I have an XML file, how do I supply it to ISOLDE? Simply open it from ChimeraX? Or do I need to place it in a specific directory? (Looking around, I see ~/.local/share/ChimeraX/1.7/isolde_data/openmm that looks relevant, but not sure this is how it's supposed to work).

Thanks again,

Guillaume

Yes, I'm afraid the coordinated metal makes it a lot more complicated (ANTECHAMBER doesn't handle anything with metals). :(

The "right" way to do this is to do a full QM-based parameterisation (see e.g. https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php), but in general that's a pretty painfully involved task and usually overkill for this application.

There is a set of AMBER-compatible parameters published (https://onlinelibrary.wiley.com/doi/10.1002/jcc.23016) which could probably be adapted (provided as text in the supp. info PDF), but they're in the GROMACS format which I'm afraid I have no experience with. I don't really have the free time right now to muddle through trying to convert these, but if you can figure out the conversion (or find someone with the right know-how to help) this is probably the most painless path to getting you moving. The other, more hacky approach is to use ANTECHAMBER to parameterise the non-metal component, then hand-edit the file to add the magnesium. It's been a while, but if I recall correctly that's the approach I took for the bacteriochlorophylls in 7o0u and its relatives... worked pretty well in general. You'll want to do a little editing of the charges (the aromatic system spreads things out so the charge on the Mg is much lower than +2 - just make sure that the overall charge on the molecule remains exactly zero.

Oh - and to actually work with the result in ISOLDE you'll need to "promote" the metal coordination bonds to true bonds (just ctrl-click on the Mg, ctrl-shift-click on an adjacent nitrogen, and use the command "bond sel").

On Wed, Apr 24, 2024 at 3:43 PM Guillaume Gaullier <guillaume.gaullier@kemi.uu.se> wrote:

Hi Tristan and chimerax-users,

Some time ago I asked the list about modeling PTM and got several helpful answer, including this one: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/5DCV4ISWC3C2R3LLAV6WRN3MBY44ETQT/

Now, I am working on a structure containing chlorophyll A molecules (residue code CLA) and realized that it won’t work for MDFF in ISOLDE because there is no MD template for it. After trying to manually fit one of these molecules rigidly, I concluded that I would rather spend the rest of the month learning how to make an MD template for it (than next month painstakingly fitting every single molecule manually rigidly).

From the message linked above, I think this should be doable because this time it is not a covalent modification on an otherwise parameterized residue, but simply a new ligand (ok, maybe the coordinated Mg2+ makes it a bit more complicated?). I looked up ANTECHAMBER, and also some documentation from OpenMM, but that got me nowhere, mostly because I have little clue what the task really entails.
My guess is that I need some program to take the CLA residue in PDB or mmCIF format (which I can easily save from a previous PDB entry) and write out an OpenMM XML file like the one you sent me back then for KCX. Is this correct? The ANTECHAMBER documentation mentions many programs and formats, and I got totally confused.

If you have time to elaborate a bit on the specific practical steps to take (including how to supply the final XML file to ISOLDE), that would be super helpful!
I can do with pointers to documentation, not afraid to read, but I need help getting oriented.

Thank you in advance!

Guillaume

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