[gmx-users] Invalid order for directive bondtypes

[Mark Abraham]

You're including that file from somewhere that violates the rules in
chapter 5. But only you know where.

Mark
On Nov 26, 2013 11:07 AM, "Elham Gholamrezai" <elham.gholamrezai at yahoo.com>
wrote:

> Dear all
>
>  I am working on simulation of hydrogen adsorption on
> graphene sheet, and I need to adopte my force field parameters, new
> force field folder is made and put in top directory of gromacs. For this
>  reason, I modified "charmm27.ff" and included new files (bond.itp,
> nonbond.itp, n2t, atp, rtp, force field.itp) in it first, then topology
> file was produced by g_x2top command without any error. But when I
> grompp for minimization, I got the following error. How can I solve it? I
>  used this command for grompp
>
>
>  grompp -f em.mdp -c conf.gro -p topol.top -o em.tpr -n index.ndx
>
> (also conf.gro include hydrogen and graphene sheet)
>
>
> Fatal error:
> Syntax error - File ffbonded.itp, line 1
> Last line read:
> '[ bondtypes ]'
> Invalid order for directive bondtypes
>
> this is my ffbonded.itp:
>
> [ bondtypes ]
> ; i      j       func       b0      kb
> C     C        1        0.1375   0.0
> C     H        1        0.108    0.0
>
> [ angletypes ]
> ; i      j      k      func      th0      cth       ub0      cub
> C     C      C       5       120.00   0.0     0.24162  29288.0
> C     C      H       5       120.00   0.0     0.21525  18409.6
>
> [ dihedraltypes ]
> ; i      j      k       l      func    phi0    cp      mult
> C      C      C       C      9       180.00  0.0     2
> C      C      C       H      9       180.00  0.0     2
> H      C      C       H      9       180.00  0.0     2
>
>
> and this is the first line of topol.top file
>
> ;
> ;    File 'topol.top' was generated
> ;    By user: onbekend (0)
> ;    On host: onbekend
> ;    At date: Mon Nov 25 23:10:04 2013
> ;
> ;    This is a include topology file
> ;
> ;    It was generated using program:
> ;    Generated by x2top
> ;
> ;    Command line was:
> ;    g_x2top -f a.gro -o topol.top -ff select
> ;
> ;    Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "final.ff/forcefield.itp"
>
>
> any help is appreciated.
> --
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