[gmx-users] Problem running grompp

[Mark Abraham]

Edward M wrote:
> 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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Mark