Dear all,

I am trying to run an enzyme system nad have to determine the rate of oxygen diffusion into the system. I have the enzyme without oxygen and have read papers where they say, it was prepared on VMD. Does anyone on the grou have experience of preparing the system? I will later run it on GROMACS.

I also have aquestion on the oxygen structure. wI tried downloading the one in PUBChem but it does not look right. it appears as a straignt line.

any help is appreciated.

Thank you