Dear GROMACS Community
Please help me with an issue i am facing in applying forcefields to mRNA. I am using 8OIV pdb. It has 5’ mRNA cap (m7GTP) linked with triphosphate bridge and then GAAA nucleotides (chain name GTG). The problem is charmm-gui cannot recognize m7GTP, however when i changed the name to 7MG, other nucleotides get lost in solution builder. Or if I try to save RNA (GAAA) m7GTP get lost in the solution builder. How can i use use this complete mRNA patch (m7GTP-GAAA) for my GROMACS simulation?
Thanks in advance for helping.
Assim Verma