Dear gmx users, I am trying to simulate a complex consisting of DNA and a protein. One chain is methylated at C. The methylated cytosine is included in the newest Charmm36 forcefield as D5MC, yet somehow when I do "gmx pdb2gmx" Gromacs does not recognize the methylated C as part of the DNA but takes it as "Other" and it breaks my DNA into different chains. Any thoughts on how I could avoid D5MC being recognized as "Other" and correctly take it as "DNA"? Thank you.
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