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 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 Thanks a lot -- 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.
