[gmx-users] A problem with grompp

[Mark Abraham]

Ken Rotondi wrote:
> These problems are typically due to grompp not finding cpp (make sure 
> it's in your path) or having opened the top file in some non-linux text 
> editor. Open the top file in vi and see if you see '*M^*' where you 
> would expect line breaks. If so your top file is polluted. To change 
> from mac line breaks to unix use:
> 
> tr '\015' '\012' <bad.top> fixed.top
> 
> Where '\015' is the mac line break and '\012' is the unix. If it's a 
> windows prob. you'll have to google for the windows line break code. 
> 
> I have had occasions where the above did not fix the solution, very 
> frustrating. If nether of the above fix the problem just re-create your 
> .mdp file in vi, this always fixes this problem.

On recent Linux platforms, you can use dos2unix and unix2dos to do those 
conversions in-place. No idea about Mac.

Mark