[gmx-users] How to solve this fatal error?
حلیمه میرسالاری
h.mirsalari66 at gmail.com
Tue Jan 23 23:15:58 CET 2018
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
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[ 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
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