[gmx-users] Problem running grompp

[Edward M]

grompp -f md.mdp -c EcPCK_b4em.gro -p EcPCK.top -o EcPCK_md

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling /usr/bin/cpp...
In file included from /storage/sw/gmx/share/top/ffamber03.itp:20,
                 from EcPCK.top:11:
/storage/sw/gmx/share/top/ffamber03bon.itp:539:22: warning: ISO C requires
whitespace after the macro name
/storage/sw/gmx/share/top/ffamber03bon.itp:541:22: warning: ISO C requires
whitespace after the macro name
/storage/sw/gmx/share/top/ffamber03bon.itp:542:22: warning: ISO C requires
whitespace after the macro name
/storage/sw/gmx/share/top/ffamber03bon.itp:545:21: warning: ISO C requires
whitespace after the macro name
/storage/sw/gmx/share/top/ffamber03bon.itp:556:19: warning: ISO C requires
whitespace after the macro name
processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
Cleaning up temporary file gromppsmKvpZ
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1108

Fatal error:
[ file "/storage/sw/gmx/share/top/spc.itp", line 41 ]:
             Atom index (1) in settles out of bounds (1-0)
-------------------------------------------------------

"You Crashed Into the Swamps" (Silicon Graphics)
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