[gmx-users] grompp

[Mark Abraham]

Michal Walczak wrote:
> Hi there!
> 
> I wanted to convert *. mdp file to get .tpr file and have changes in
> *.top so I put down such a command: grompp -f fullmd_sol.mdp -c
> minimized_water.gro -p aki.top -o fullmd.tpr . One fatal error occured
> saying that there was error ie\\with proccessing input file. It worked
> fine for protein, but now for 3 aa peptide it got stuck. Which input
> was incorrect? What should I do now ?

The same .top won't work for both a protein and a 3 aa peptide.

Otherwise, you'd better consult your nearest mind-reader, or actually 
tell us the error message from grompp. :-)

Mark