Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4# checking input for internal consistency... calling /marie/bin/cpp... In file included from /home/marie/gromacs-3.3/share/tutor/aladip/../../../share/top/ffamber99p.itp:19, from aladip.top:11: /home/marie/gromacs-3.3/share/tutor/aladip/../../../share/top/ffamber99pbon.itp:517:22: warning: ISO C requires whitespace after the macro name /home/marie/gromacs-3.3/share/tutor/aladip/../../../share/top/ffamber99pbon.itp:519:22: warning: ISO C requires whitespace after the macro name /home/marie/gromacs-3.3/share/tutor/aladip/../../../share/top/ffamber99pbon.itp:520:22: warning: ISO C requires whitespace after the macro name /home/marie/gromacs-3.3/share/tutor/aladip/../../../share/top/ffamber99pbon.itp:523:21: warning: ISO C requires whitespace after the macro name /home/marie/gromacs-3.3/share/tutor/aladip/../../../share/top/ffamber99pbon.itp:534:19: warning: ISO C requires whitespace after the macro name processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Cleaning up temporary file gromppiZbKU7 ------------------------------------------------------- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1108 Fatal error: [ file "/home/marie/gromacs-3.3/share/tutor/aladip/../../../share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) -------------------------------------------------------