[gmx-users] grompp problem

Chris Neale chris.neale at utoronto.ca
Fri Jan 25 15:49:27 CET 2008

>>>/ Hello!
/>>/ I've tried to prepare a file for the mdrun and when I use grompp I get the
/>>/> massage that there is a fatal error in grompp.c line 1111 or line 1109,
/>>/> respectively.
>/>What command are you issuing?  What's in the .mdp file?  What is the *exact*
/>>/error message?
/>>/Without this kind of information, you'll get no useful advice.
/>>>/ Thank you very much in advance
/>/> >Jens
/>Hello Justin,
>My commands for grompp were:
>grompp -f ../grompp.mdp -po test -c test -p test -pp test_pp -o test
>The grompp.mdp file is the one that can be found in the manual (long version with coments) and the output of grompp was:
>Program grompp, VERSION 3.3.1
>Source code file: grompp.c, line: 1109
>Fatal error:
>There were 1 error(s) processing your input

My guess is that your .mdp file is in windows format with carriage returns. Try fixing that, or at least testing it
based on what is here:

Note that you still did not provide nearly enough info. I suggest that you run grompp then copy the entire span including your 
command 'grompp...' to the end of the output.

Also, I just did a search for your error message:
Source code file: grompp.c, line: 1109
on the gromacs search site and the first link is this:
and the next one in that thread is a putative solution.

I suggest that look through your output and try to find the error / warning messages and search them.


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