I would like to carry out a simulation of insulin on a silica surface. I have devised the following procedure to carry out the necessary simulation but would like to know if I am missing out anything.
Firstly, use the CHARMM gui pdb reader so that I can select the correct insulin monomer (as it allows you to select just chains A and B from a dimer or hexamer model) and have it in the correct protonation state.
Secondly, use the CHARMM gui nanomaterial builder to make a silica that is of the right size and protonation state. VMD to position protein correctly, save as pdb.
Thirdly, use the Multi Component Assembler to combine the two files generated from steps 1 and 2.
From here on use the files generated to carry out a simulation on Ubuntu.
Is this the correct procedure to carry out a viable simulation?
I would like to orientate my protein onto the surface of the silica. Does the Multi - Component Assembler do this or can I just merge the two PDB files from VMD and then carry out a simulation on Ubuntu?
I am relatively new to this and any advice would be much appreciated and go a long way to helping me understand.