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 ? Regards KT On Mon, Dec 17, 2012 at 9:31 PM, Justin Lemkul <[email protected]> wrote: > > > On 12/17/12 9:24 AM, Kieu Thu Nguyen wrote: > >> Dear All, >> >> When i do the "Step Four: Adding Ions"in the tutorial "KALP-15 in DPPC", >> it >> appears the error: >> >> Fatal error: >> No such moleculetype W >> >> I checked .top file and included.itp files, they have definded water >> molecule type name is "W". >> >> What happens ? >> >> > There's got to be something wrong with what's #included or how it's named. > The error is pretty straightforward. > > Also note that you are not, in fact, doing the tutorial - you are > following its suggested method with some different system. I cannot > guarantee that the tutorial is suited for whatever you're trying to do. > The workflow might be similar, but other aspects (practical > considerations, .mdp files, etc) may be different. > > -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
