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

[Kieu Thu Nguyen]

I have just found the right group is 15 (SOL) :-)

Thanks so much and sorry about my stupid question !


On Mon, Dec 17, 2012 at 11:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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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