normal Nucleic acid simulation with Martini3

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1 year 4 months ago #8916 by devP
Hi,

I wanted to do a CG-simulation to study protein-RNA interaction. with the current release of martini I can find the parameters for nucleobases, but I do not know how to generate a CG model for nucleic acids for martini3. The martinize2 script does not seems to recognize RNA residues yet, is it possible to modify it to recognize these residues and generate a CG model?

Please help me with this.

Thanks

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1 year 4 months ago #8918 by peterkroon
Replied by peterkroon on topic Nucleic acid simulation with Martini3
Hi,

martinize2 reads all forcefield parameters from external datafiles, so yes, you can add these.
You can either add the required files in the installation folder (probably /usr/local/lib/python3.x/dist-packages/vermouth/data). Alternatively, use the -map-dir and -ff-dir options of martinize2. My suggestion is to make a copy of the current martini3001 ff in a working directory, rename it to e.g. martini3001+nucleic, and point martinize2 to it with the CLI flags.

For the files to add, you'll need to add the data in 3 places:
- in the origin/from force field (default 'universal'). This is used to guess the bonds in your pdb based on atom names, and to add missing atoms and such. Copying over a charmm rtp file should do the trick. Also take a look at how (protein) termini are implemented in modifications.ff.
- in the destination/to force field (default 'martini3001'). These are the parameters that end up in your output itps. You'll need to add both the residue/block parameters, as well as the parameters *between* them. The latter are called 'Link's. Again, also look at the termini.
- in the mappings, to teach martinize2 which atoms in the input (universal) map to which in the output (martini3001).

Unfortunately there is no documentation or tutorial available yet that describe the file formats, so you'll have to reverse engineer it based on the existing files.
Be sure to check your resulting itps for the following:
- missing bonds/interactions between residues. Especially the protein-DNA bonds.
- termini. You will probably need to add something like `-modify B-ADE1:5-ter` to apply a 5-ter modification to residue ADE with resid 1 in chain B.

Good luck! (:
Follow up questions welcome!

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11 months 2 weeks ago #9109 by Nguyen
Replied by Nguyen on topic Nucleic acid simulation with Martini3
Dear Peterkroon,

As your suggestion, we have two ways to generate a topology for RNA in combination with protein from the source code of martini3, right? I'm trying to set up a protein-RNA complex and I have been facing with how to generate a topology for RNA from matini2. Could you write something clearly or give me a tutorial for it.
Thank you so much

Best,

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