[gmx-users] error "No such moleculetype W"
jalemkul at vt.edu
Mon Dec 17 17:40:26 CET 2012
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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