[gmx-users] Generating topology for a hem protein

[zeineb SI CHAIB]

Dear all, 

I'm desperetly looking for help to generate the topology of my hem protein. 


	
	
	
	I'm using CHARMM as a force field and apparently PDB2gmx assigns dihedrals that should not exist and it's complicated to verify everything. Justin suggested using CHARMM-GUI, I followed a tutorial that I found on line (http://cermm.concordia.ca/workshopDocs/CHARMM/Lague.pdf) in order to build my system, I'm in the final step, adding the Hem group to my protein but I don't know how to do it and I don't know if all the steps went well or not. 

Any advices, HELP please!! I'll really appreciate your help, time and patience! 

Regards. 

Zeinbe.