Hi, The only thing I can think of is that you've run pdb2gmx already and added the termini (adding H1 H2 and H3 for the terminus, which causes the complaints). Now, you're running pdb2gmx for the second time (right?) to merge the chains. Next to -ignh you can also try to simply remove these N-terminal protons pdb2gmx is complaining about.
Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
