[gmx-users] (no subject)

[Mark Abraham]

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.mirsalari66 at 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
>
>
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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
> --
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