[gmx-users] error "No such moleculetype W"

[Justin Lemkul]

On 12/17/12 11:38 AM, Kieu Thu Nguyen wrote:
> Thank Justin ! I found my mistake. But when i type the next command line
>
>   genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
> CL -nn 4
>
> and choose group 0 (system), the error is
>
> Fatal error:
> No line with moleculetype 'System' found the [ molecules ] section of file
> 'topol.top'
>
> the section [molecules] in my tolpol.top file is
>
> [ molecules ]
> ; Compound        #mols
> Protein                1
> DPPC                126
> SOL                  15628
>
> Should i add "System" into topol.top file ?
>

Absolutely not.  Read what genion does - it replaces solvent molecules with 
ions.  If you choose System (which you can't, because that's a group, not a 
[moleculetype]) you'll start haphazardly replacing random molecules with ions. 
Definitely not what you want.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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