[gmx-users] problem with genion

Siavoush Dastmalchi Dastmalchi.s at tbzmed.ac.ir
Thu Feb 21 11:18:37 CET 2008

Hi again,
The genion doesn't work. I issue the following:
$ genion -s fullmd.tpr -random -nname Cl -nn 8 -o out.gro -p test.top -g genion.log
and get the error massage of:
Processing topology
Program genion, VERSION 3.3.1
Source code file: futil.c, line: 340
File input/output error:
If I don't use -p test.top in the command line, then it doesn't complain, but it stops after selecting the group and doesn't move forward.
Group    11 ( Non-Protein) has 44823 elements
Group    12 (         SOL) has 44823 elements
Group    13 (       Other) has 44823 elements
Select a group: 12
Selected 12: 'SOL'
Number of (3-atomic) solvent molecules: 14941
Replacing solvent molecule 1752 (atom 6577) with Cl
Any idea?
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