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 <[email protected]> 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> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
