[gmx-users] Invalid order for directive bondtypes

[Mark Abraham]

You probably need to define [atomtypes] before you can define [bondtypes]
that use them. So swap the order of your #include statements.

Mark

On Mon, Oct 6, 2014 at 6:18 AM, Atila Petrosian <atila.petrosian at gmail.com>
wrote:

> Dear gromacs users
>
> I want to do MD simulation of a CNT.
>
> I used aromatic carbon from charmm.ff
>
> I created a cnt.ff folder containing following files:
>
> ffcnt.atp:
> -----------
> CA    12.01100 ;    aromatic C
> -------------------------------------------------------------------------
> ffcnt.n2t:
> -----------
> C    CA    0.00     12.011    3    C 0.141   C 0.141   C 0.141
> C    CA    0.00     12.011    2    C 0.141   C 0.141
> -------------------------------------------------------------------------
> ffcntbonded.itp:
> --------------------
> [ bondtypes ]
> ; i      j       func       b0      kb
> CA      CA        1        0.1375   0.0
>
> [ angletypes ]
> ; i      j      k      func      th0      cth       ub0      cub
> CA      CA      CA       5       120.00   0.0     0.24162  29288.0
>
> [ dihedraltypes ]
> ; i      j      k       l      func    phi0    cp      mult
> CA      CA      CA      CA      9       180.00  0.0     2
> -------------------------------------------------------------------------
> ffcntnonbonded.itp:
> -------------------------
> [ atomtypes
> ]
> ;name    at.num    mass    charge    ptype    sigma
> epsi
> CA       6        12.01100        0.00    A       0.335
> 0.234463
> -------------------------------------------------------------------------
> ffcnt.rtp:
> ----------
> [ bondedtypes
> ]
> ; Col 1: Type of
> bond
> ; Col 2: Type of
> angles
> ; Col 3: Type of proper
> dihedrals
> ; Col 4: Type of improper
> dihedrals
> ; Col 5: Generate all dihedrals if 1, only heavy atoms of
> 0.
> ; Col 6: Number of excluded neighbors for nonbonded
> interactions
> ; Col 7: Generate 1,4 interactions between pairs of hydrogens if
> 1
> ; Col 8: Remove propers over the same bond as an improper if it is
> 1
> ; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14
> RemoveDih
>      1       5          9        2        1           3      1
> 0
>
>
> [ ALA
> ]
>  [ atoms
> ]
>     N    NH1    -0.47
> 0
>     HN    H    0.31
> 1
>     CA    CT1    0.07
> 2
>     HA    HB    0.09
> 3
>     CB    CT3    -0.27
> 4
>     HB1    HA    0.09
> 5
>     HB2    HA    0.09
> 6
>     HB3    HA    0.09
> 7
>     C    C    0.51
> 8
>     O    O    -0.51
> 9
> .
> .
> .
> -------------------------------------------------------------------------
> forcefield.itp:
> ----------------
> #define _FF_CNT
>
> [ defaults ]
> ; nbfunc    comb-rule    gen-pairs    fudgeLJ    fudgeQQ
>     1           2          yes           1.0    1.0
>
> #include "ffcntbonded.itp"
> #include "ffcntnonbonded.itp"
> -------------------------------------------------------------------------
>
> After creating cnt.top file using g_x2top, I used grompp for energy
> minimization, but I encountered with Fatal Error:
>
> Syntax error - File ffcntbonded.itp, line 1
> Last line read:
> '[ bondtypes ]'
> Invalid order for directive bondtypes
>
> Before doing MD simulation, I checked carbon nanotube in the GROMACS
> website:
>
>
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube?highlight=nanotube
>
> In my opinion, my manner is true.
>
> How to solve this problem?
>
> Any help will highly appreciated.
> --
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