Gromacs+Charmm36 does not recognize methylated cytosine in protein-DNA complex?

02 February 2020 1 5K Report

I am trying to simulate a complex consisting of DNA and a protein using Gromacs. 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 two different chains. Any thoughts on how I could avoid D5MC being recognized as "Other" and correctly take it as "DNA"?

Qinghua Liao

D5MC is not a standard nucleotide in the force field library. One you can do is that you add D5MC as DNA in the file residuetype.dat, or you make a new index group,

combing the default DNA group and the Other group as one. However, you still have to be care of the connections between the nucleotide with others.

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