[gmx-users] error "No such moleculetype W"
Kieu Thu Nguyen
kieuthu2212 at gmail.com
Mon Dec 17 17:52:49 CET 2012
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
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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