[gmx-users] Genion cannot read from input

Nathan Bullock bullocknathan534 at gmail.com
Sat Apr 27 17:21:54 CEST 2013

I am running genion neutralize the charge of my protein.
I got an error that wasn't very descriptive
Fatal error:
Cannot read from input
The part of the script that called this program read as follows
/usr/local/gromacs-4.5.5/bin/grompp -f em.mdp -c filled_box.pdb -p
protein_mod_filled5.top -o ions.tpr
/usr/local/gromacs-4.5.5/bin/genion -s ions.tpr -o solv_ions.pdb -p
protein_mod_filled5.top -pname NA -nname CL -nn 3
I am using the amber03 force field.
I had read on some of the pages that different forcefields used different
nomenclature for the ions used to neutralize the charge.

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