Hi, Either your topology components are in the wrong order (like the message says) or you're doing something strange. Notice how your water won't have any atoms unless _FF_CHARMM is defined, which will only be defined if you've got a charmm force field involved. But nobody's got enough information to help you.
And please do yourself a favour and get a more recent GROMACS version installed. It's been more than 7 years since 4.5.5... Mark On Wed, Jan 24, 2018 at 10:45 AM حلیمه میرسالاری < h.mirsalar...@gmail.com> wrote: > Dear all > > l am using gromacs 4.5.5 version for simulation carbon nanotubes with > charmm27 force feild ,there was no error grompp stage,but when l do > simulation of carbon nanotube in tip3p water encountered with > fatal error: > > [ file tip3p.itp, line 40]: > Atom index (1) in settles out of bounds (1-0). > This probably means that you have inserted topology section "settles" > in a part belonging to a different molecule than you intended to. > In that case move the "settles" section to the right molecule. > > Please guide me > > File:tip3p.itp > > Thanks > > Halimeh > > > 1 > 2 > 3 > 4 > 5 > 6 > 7 > 8 > 9 > 10 > 11 > 12 > 13 > 14 > 15 > 16 > 17 > 18 > 19 > 20 > 21 > 22 > 23 > 24 > 25 > 26 > 27 > 28 > 29 > 30 > 31 > 32 > 33 > 34 > 35 > 36 > 37 > 38 > 39 > 40 > 41 > 42 > 43 > 44 > 45 > 46 > > [ moleculetype ] > ; molname nrexcl > SOL 2 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > #ifdef _FF_CHARMM > 1 OWT3 1 SOL OW 1 -0.834 > 2 HWT3 1 SOL HW1 1 0.417 > 3 HWT3 1 SOL HW2 1 0.417 > #endif > > > #ifdef FLEXIBLE > > #ifdef CHARMM_TIP3P > [ bonds ] > ; i j funct length force.c. > 1 2 1 0.09572 376560.0 0.09572 376560.0 > 1 3 1 0.09572 376560.0 0.09572 376560.0 > > [ angles ] > ; i j k funct angle force.c. > 2 1 3 1 104.52 460.24 104.52 460.24 > #else > [ bonds ] > ; i j funct length force.c. > 1 2 1 0.09572 502416.0 0.09572 502416.0 > 1 3 1 0.09572 502416.0 0.09572 502416.0 > > [ angles ] > ; i j k funct angle force.c. > 2 1 3 1 104.52 628.02 104.52 628.02 > #endif > > > #else > [ settles ] > ; i j funct length > 1 1 0.09572 0.15139 > > [ exclusions ] > 1 2 3 > 2 1 3 > 3 1 2 > #endif > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.