Hi Andrea,
this is my input for the minimization:
#Minimisation
grompp -f EM.mdp -c 1KAL_SOLV.pdb -p 1kal.top -o 1KAL_MINI.tpr mdrun -s
1KAL_MINI.tpr -o 1KAL_MINI.trr -x 1KAL_MINI.xtc -c 1KAL_MINI.pdb -v -e
1KAL_MINI.edr
Giacomo
andrea spitaleri wrote:
Hi Giacomo,
you are using the flag -c twice. Check your input line in the shell.
See mdrun -h for more information.
It should be something like:
mdrun -s file.tpr -o file.trr -c file.pdb
probably you have
mdrun -s file.tpr -o file.trr -c -c file.pdb
-------------------------------^
a typo error
Regards
Andrea
Giacomo Bastianelli wrote:
Hi David,
is there an error in the souce code file????
ps.sorry if the question is stupid but I am very
naive to bioinformatic as well...
Giacomo
David van der Spoel wrote:
Giacomo Bastianelli wrote:
Hi Tsjerk,
I have just fixed the problem of cyclic (manually deleted some bonds
that gromacs added...), I got everything ready for the minimization
step after genbox.
I run it and it says:
Program grompp, VERSION 3.3
Source code file: statutil.c, line: 549
Fatal error:
Double command line argument -c
Is there anything wrong with my inputs?
thanks a lot
yes. it is exactly what it says.
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