[gmx-users] Group protein not found in indexfile

[Steve Seibold]

Hello
I am just trying to do a simple MD on a dimmer system (in which the dimmers are NOT identical). I can use pdb2gmx to create a topology file and four .itp files:::: pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and system.Protein.chainX.itp.

When I use grompp  however, I get a fatal error “Group protein not found in index file. Maybe you have non-default groups in  your .mdp file,  while not using ‘-n’ option in grompp”

I’ve looked up this error on-line but I don’t see people getting this error when using multiple chains. I only have protein present and nothing  else. I am obviously doing something incorrect.

I would greatly appreciate any comments that would help me..

Thanks.