GROMACS version:2020
GROMACS modification: Yes/No
Here post your question I applied md simulation on my dna-ligand system but I prepared input files using charmm-gui.my simulation has finished sucessfully.for analysis I have a problem
my defaults groups not include DNA or backbone so,how to create DNA groups
Could anybody give me some option inorder to crete DNA groups
Merge groups 2-5 to create the full DNA, from which you can define the backbone however you like (there are different conventions for this with DNA, so it’s up to you).
Please can you help me with your DNA ligand protocol. I tried simulating DNA ligand complex but results are not good. Need help.