[gmx-users] Genion cannot read from input

Justin Lemkul jalemkul at vt.edu
Sat Apr 27 18:28:44 CEST 2013

On 4/27/13 11:21 AM, Nathan Bullock wrote:
> 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

Was ions.tpr successfully generated?

> /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.

This is no longer true as of Gromacs 4.5, which has standardized nomenclature. 
You can always check ions.itp for your force field to be sure.

The "cannot read from input error" only arises if (1) you are specifying a 
nonexistent index group (not applicable here) or (2) presumably if some input 
file does not exist.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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