[gmx-users] grompp problem

[Chris Neale]

>>>/ 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.
/>>/
/>>/-Justin
/>>/
/>>>/
/>>>/ 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
>-------------------------------------------------------
> 
>Jens

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:
http://www.gromacs.org/pipermail/gmx-users/2007-July/028457.html


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:
http://www.gromacs.org/pipermail/gmx-users/2008-January/031877.html
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.

Chris.