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
========================================
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