[gmx-users] General questions about topology building

[Marko Sever]

So the following question, if I want to change a few residues in a system that is already made (equilibrated, a protein in a lipid membrane), how should i go about that? What would be the protocol?

I did it this way -> i first made a pdb out of the last frame (changed the 3 residues in Chimera) and then went about with pdb2gmx ,  but I got snagged with a problem, even tho' the pdb has all the hydrogens gromacs says it doesn't have all of them in one cholesterol molecule and doesn't want to correctly construct the topology. Is it maybe the "TER" part that is between the different molecules in the pdb? (The protein and the different lipids)

Is there a better way to do it?

Also how do I sequentially build topology, that I build it separately for the protein and separately for the membrane for example and then put them together?

Thank you!
Marko