[gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain

[i.ilie at bioc.uzh.ch]

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.

Best,
Ioana