[gmx-users] x2top_error

[Alex]

x2top is finding atoms with more nearest neighbors than what you have in
your ff. Make sure the box that contains your CNT is of appropriate size,
especially along the CNT axis.

Alex

On Mon, Jul 16, 2018 at 3:10 PM, Atila Petrosian <atila.petrosian at gmail.com>
wrote:

>  Hi gromacs users,
>
> I used following command for CNT.
>
> gmx_mpi x2top –f cnt.gro –o cnt.top –ff cnt –name CNT –pbc -noparam
>
>
> I encountered with:
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> Can not find forcefield for atom CA-968 with 5 bonds
>
> Can not find forcefield for atom CA-970 with 5 bonds
>
> Can not find forcefield for atom CA-971 with 1 bonds
>
> Can not find forcefield for atom CA-972 with 5 bonds
>
> Can not find forcefield for atom CA-974 with 5 bonds
>
> Can not find forcefield for atom CA-975 with 1 bonds
>
> Can not find forcefield for atom CA-976 with 5 bonds
>
> Can not find forcefield for atom CA-978 with 5 bonds
>
> Can not find forcefield for atom CA-979 with 1 bonds
>
> Can not find forcefield for atom CA-980 with 5 bonds
>
> Can not find forcefield for atom CA-982 with 5 bonds
>
> Can not find forcefield for atom CA-983 with 1 bonds
>
> Can not find forcefield for atom CA-984 with 5 bonds
>
> Can not find forcefield for atom CA-986 with 5 bonds
>
> Can not find forcefield for atom CA-987 with 1 bonds
>
> Can not find forcefield for atom CA-988 with 5 bonds
>
> Can not find forcefield for atom CA-990 with 5 bonds
>
> Can not find forcefield for atom CA-991 with 1 bonds
>
> Can not find forcefield for atom CA-992 with 5 bonds
>
> Can not find forcefield for atom CA-994 with 5 bonds
>
> Can not find forcefield for atom CA-995 with 1 bonds
>
> Can not find forcefield for atom CA-996 with 5 bonds
>
> Can not find forcefield for atom CA-998 with 5 bonds
>
> Can not find forcefield for atom CA-999 with 1 bonds
>
> Can not find forcefield for atom CA-1000 with 5 bonds
>
> Can not find forcefield for atom CA-1002 with 5 bonds
>
> Can not find forcefield for atom CA-1003 with 1 bonds
>
> Can not find forcefield for atom CA-1004 with 5 bonds
>
> Can not find forcefield for atom CA-1006 with 5 bonds
>
> Can not find forcefield for atom CA-1007 with 1 bonds
>
> Can not find forcefield for atom CA-1008 with 5 bonds
>
>
>
> I have a directory (cnt.ff) in current directory and the content of n2t
> file is as follows:
>
> 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
>
> How to resolve this error?
> --
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