Thank you very much David Cuong
On 18 February 2013 17:40, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 2013-02-18 10:16, Cuong Nguyen wrote: > >> Dear Gmx-users, >> >> I have ions.itp file for polarized Na+ and Cl- as follows: >> >> >> ; Sodium, Na+ >> [ moleculetype ] >> ; molname nrexcl >> Na+ 1 >> >> [ atoms ] >> ; id at type res nr residu name at name cg nr charge >> 1 Nac 1 Na+ Nac1 1 +0.312403 >> 2 Nas 1 Na+ Nas1 1 +0.687597 >> >> [ polarization ] >> ; See notes above. alpha (nm^3) >> 1 2 1 0.00024 >> >> [ exclusions ] >> ; iatom excluded from interaction with i >> 1 2 >> 2 1 >> >> ; Chloride, Cl- >> [ moleculetype ] >> ; molname nrexcl >> Cl- 1 >> >> [ atoms ] >> ; id at type res nr residu name at name cg nr charge >> 1 CLc 1 Cl- CLc1 1 -4.457187 >> 2 CLs 1 Cl- CLs1 1 +3.457187 >> >> [ polarization ] >> ; See notes above. alpha (nm^3) >> 1 2 1 0.00325 >> >> [ exclusions ] >> ; iatom excluded from interaction with i >> 1 2 >> 2 1 >> >> and after running the command: >> >> *grompp -f ions.mdp -o min.tpr -c box1.g96* >> >> >> it appears the error: >> >> Program grompp, VERSION 4.5.5 >> Source code file: topio.c, line: 656 >> >> Fatal error: >> Syntax error - File ions.itp, line 20 >> Last line read: >> '[ exclusions ]' >> Invalid order for directive exclusions >> >> Please help me to deal with this issue? >> > remove the exclusions. Since there are no bonds you can not have > exclusions. Exclusions will nevertheless be generated. Please check the > topology using gmxdump. > > >> Thanks a lot in advance. >> >> Best regards, >> >> Cuong >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
