DNA is not implemented yet?

[songyongshun]

It seems the martinze2 cannot recognize the DNA.
The error is
WARNING - unknown-residue - Can't add bonds based on atom names for residue A-DT1 because 'Residue DT is not known to force field charmm'. Falling back to distance criteria.

[pckroon]

@fgrunewald I seem to remember we used to have DNA but it got removed a while ago for a good reason. I just can't remember the reason. Do you remember?

Either way, @songyongshun you can try to add the required files on your local installation. Do be sure to check the resulting ITP very carefully. One of the things I know are an issue is with the elastic network. It's (currently) not possible to use different parameters for the elastic network for different parts of your system (e.g. proteins and dna), while the respective models do need different parameters....

[fgrunewald]

@pckroon the issue is / was that Martini2 DNA itp files are somewhat different in terms of EN depending on the martinize-dna version. To make things more complicated not all EN options are currently stable - reason unknown. Finally, repair graph takes ages to repair nucleobases unless they already contain all hydrogen-atoms and proper labels, but that's more an implementation detail. I even have all files lying around somewhere. If I find the time I'll add them to the repro again using the conventions we settled on for polyply.

Polyply has a working Martini2 DNA implementation for single stranded and we're currently expanding it to dsDNA. @songyongshun if you need M2 DNA especially for large structures feel free to open a discussion here.