[gmx-users] x2top & Encad all-atom force field (vacuum) not recognizing bonds

[darrellk at ece.ubc.ca]

Dear All,
I have been trying to determine why I am experiencing problems when I run
a gromacs file through x2top. I have checked my gromacs file with VMD to
ensure that the file is correct and VMD validates that my file is
correct as I see the intended structure. Thus, the atoms are indeed
located within reasonable distance from each other such that x2top
should be recognizing the bonds.

Here is an extract from my gromacs file:

    2Grph C        1   0.000   0.000   0.000  0.0000  0.0000  0.0000
    2Grph C        2   0.071  -0.123   0.000  0.0000  0.0000  0.0000
    2Grph C        3   0.071   0.123   0.000  0.0000  0.0000  0.0000
    2Grph C        4  -0.142   0.000   0.000  0.0000  0.0000  0.0000
    2Grph C        5  -0.000  -0.250   0.000  0.0000  0.0000  0.0000
    2Grph C        6   0.210  -0.120   0.000  0.0000  0.0000  0.0000

I thought that in order to make x2top work correctly that I would have to
modify the files as described in Christopher Stiles website
(http://cs86.com/CNSE/SWNT.htm). I made the specified changes to the
following files and saved them in my working directory:
ffencadv.n2t
ffgmx.n2t
ffgmxbon.itp

I also changed the name of ffgmxbon.itp to ffencadvbon.itp as I read in
one post that this file should be renamed as such.

After all these changes, I still experience a problem when I run the
command:
x2top -ff select -f graphene_nm.gro -o graphene_nm.top
selecting option  7: Encad all-atom force field, using scaled-down vacuum
charges

When I run the above command, I receive output telling me that the atoms
have 0 bonds. An extract of the output appears below for your reference.
Can not find forcefield for atom H-266 with 0 bonds
Can not find forcefield for atom H-267 with 0 bonds
Can not find forcefield for atom H-268 with 0 bonds
Can not find forcefield for atom H-269 with 0 bonds
Can not find forcefield for atom H-270 with 0 bonds

-------------------------------------------------------
Program x2top, VERSION 3.3.3
Source code file: x2top.c, line: 206

Fatal error:
Could only find a forcefield type for 0 out of 270 atoms
-------------------------------------------------------

Could you please help me resolve this issue?

Thank you in advance for your assistance.

Darrell Koskinen