DNA in charmm36

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
i’m facing a problem in creating topology for dna with charmm36. That’s what i got .
Atom C7 in residue DT 2 was not found in rtp entry DT with 32 atoms
while sorting atoms.Also by modifying C7 into C5M it doesn’t work.

2

Hi Jacopo,

Indeed, C5M is Charmm36’s way of naming the methyl carbon in thymine. Did you get exactly the same error after the modification (Atom C5M in residue DT 2 was not found...)?

3

after a couple of attempts the command has worked properly.Thanks.