Mark, Thanks again for the swift reply! Stupid of me to miss that message! I noticed some other code that was generated as output of pdb2gmx, which I do not fully understand. Can you maybe explain some of it?
Processing chain 1 (4 atoms, 2 residues) Warning: Starting residue EthB1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue EthE1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. I understand the two warnings. To my directory I added a file residuetypes.dat, where I specificy that (among others) EthB and EthE (which are the ending and beginning residues of polyethylene) are Polymer. What does the rest of this message mean? I don't understand how I could fix this message? Or even what it wants to do, since i've defined my own terminal residues. Is it not possible to define my own 'group'? residuetypes.dat: EthB Polymer EthE Polymer Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.