I found another error through grompp_genion command:
command used:
grompp_d -f em -c 1chl-b4em.gro -p 1chl.top -o 1chl-4em-1.gro > grompp_b4em_agenion.output
ERROR:
Program grompp_d, VERSION 4.5.6
Source code file: grompp.c, line: 523
Fatal error:
number of coordinates in coordinate file (1chl-b4em.gro, 17266)
does not match topology (1chl.top, 17272)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
If you still struggle with this problem, please give some more info to help you.
I'm not aware of any Gromacs tool like "grompp_genion". Just two independent scripts, "grompp" and "genion". Did you already perform "genion" prior to the call you stated? Did you edit your .top or .gro file manually (deleted or added atoms)?
Furthermore, the outcome of grompp (-o) is a .tpr not a .gro file.
Greetings.
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