GROMACS version: 2020
GROMACS modification: yes
I have performed covalent docking using maestro and want to convert the files to gromacs and then perform covalent md simulation.
I have been able to run the non covalent md simulation but not been able to retain the covalent bond while making gromacs file. Please help regarding this.
You will need to parametrize the covalently modified amino acid and add it as a new residue in the force field.
Hey. Thank you for your help. I could make the disulfide bond, but the two hydrogens have merged(attached photo). Please help me with that.
That is a visual artifact. For example, VMD guesses where the bonds are based on the inter-atomic distances. So what you are seeing here is the H attached to the S on the left is bent over towards the right S. And it is close enough such that VMD thinks they should be bonded.
Check your topology around the left S and it’s H, something is probably missing.