[gmx-users] Group protein not found in indexfile

Hello I am having trouble running a dimmer invacuo simulation. I can do energy minimization on it, but when I attempt to generate md.tpr file I get this weird message about “Group Protein not found in index”. I don’t see why I would need an index file. I have no trouble generating a md.tpr

[gmx-users] Group protein not found in indexfile

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

[gmx-users] Group protein not found in indexfile

Hi Justin Thanks for your response. Here are the files you asked for. They are all text files. I am still attempting to fix this, but am still getting the error I described no matter what I have done so far. Thanks again, Stevegrompp -f pr.mdp -n pr.ndx -c prbox.pdb -p system.top -o pr.tpr --