[gmx-users] cyclic peptides

[Dallas B. Warren]

If you haven't already worked it out the error you got of 

> >>>> Fatal error:
> >>>> Double command line argument -c

Is because if the command line you used, you have two -c
switches/arguments, as informed by the error.

> #Minimisation
> grompp -f EM.mdp -c 1KAL_SOLV.pdb -p 1kal.top -o 

There is one -c on the above line.

> 1KAL_MINI.tpr mdrun -s 
> 1KAL_MINI.tpr -o 1KAL_MINI.trr -x 1KAL_MINI.xtc -c 

And then a second on the above line.

> 1KAL_MINI.pdb -v -e 
> 1KAL_MINI.edr

It appears like you have been trying to execute grompp then mdrun on the
same command line.  And that doesn't work, since grompp is the command
being run and everything else on that line tells it what to do.  You
have to have mdrun on a separate line.