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

[Kieu Thu Nguyen]

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 ?

Regards
KT


On Mon, Dec 17, 2012 at 9:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/17/12 9:24 AM, Kieu Thu Nguyen wrote:
>
>> Dear All,
>>
>> When i do the "Step Four: Adding Ions"in the tutorial "KALP-15 in DPPC",
>> it
>> appears the error:
>>
>> Fatal error:
>> No such moleculetype W
>>
>> I checked .top file and included.itp files, they have definded water
>> molecule type name is "W".
>>
>> What happens ?
>>
>>
> There's got to be something wrong with what's #included or how it's named.
>  The error is pretty straightforward.
>
> Also note that you are not, in fact, doing the tutorial - you are
> following its suggested method with some different system.  I cannot
> guarantee that the tutorial is suited for whatever you're trying to do.
>  The workflow might be similar, but other aspects (practical
> considerations, .mdp files, etc) may be different.
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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