[gmx-users] problem with genion

[Mark Abraham]

OZGE ENGIN wrote:
> Hi gromacs-users,
> 
> I have a problem with the simulation of a capped lysine residue.I followed the tutorial step by step. I added 1 Cl ion into my system in order to neutralize the overall charge by using genion, and then used the grompp command and I encountered with the following error:
> 
> Program grompp, VERSION 3.3.1
> Source code file: toppush.c, line: 891
> 
> Fatal error:
> moleculetype CU1+ is redefined
> 
> 
> What is the problem?

The molecule named CU1+ is being redefined. I'm not sure why such a 
molecule even exists in such a tutorial, but almost certainly you 
haven't followed the instructions as precisely as you needed to. If you 
don't understand how molecules get defined, have a read of the relevant 
part of chapter 5 of the manual.

Mark