I am trying to run a molecular dynamic of a protein-DNA complex with Gromacs. The problem is that the DNA is methylated and the force fields i have do not recognise mC. Does anyone have or know where to find force field parameters for mC? I've read a couple of papers and they cite CHARMM27, but the one i got does not have mC.
CHARMM supports 5-methyl cytosine. It's a very simple patch that needs to be applied to the cytosine residue entry (see PRES 5MC2 in toppar_all36_na_modifications.str, freely available from the MacKerell group website).
ATOM C5 CN3D -0.11
ATOM C5M CN9 -0.22
ATOM H5M1 HN9 0.09
ATOM H5M2 HN9 0.09
ATOM H5M3 HN9 0.09
I would advise using the newer CHARMM36, though, as there are some specific enhancements in nucleic acids that you should be using.
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