[gmx-users] x2top, error generating topology

[Vitaly Chaban]

Hello All,

I've got a problem with x2top in gromacs 3.3.3. Trying to obtain
atopology from ".pdb" structure I do the following:
1. Add
>> C C 1 C ; CNT Carbon with one bond
>> C C 2 C C ; CNT double bonded Carbon
to ffencadv.n2t.

2. Add the following lines
[ bondtypes ]
; i j func b0 kb
C C 1 0.14210 478900.

[ angletypes ]
; i j k func th0 cth
C C C 1 120.000 397.480

[ dihedraltypes ]
; i l func q0 cq
C C 1 0.000 167.360

to ffgmxbon.itp.

3. Then I execute: x2top -f cnt.pdb -o cnt.top
where cnt.pdb is from http://turin.nss.udel.edu/research/tubegenonline.html

During the processing I select
7: Encad all-atom force field, using scaled-down vacuum charges

The output is
Looking whether force field files exist
Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.rtp
Opening library file ffencadv.n2t
WARNING: all CONECT records are ignored
Opening library file ffencadv.n2t
There are 0 name to type translations
Generating bonds from distances...
atom 144
Can not find forcefield for atom C-1 with 0 bonds
Can not find forcefield for atom C-2 with 0 bonds
Can not find forcefield for atom C-3 with 0 bonds
Can not find forcefield for atom C-4 with 0 bonds
Can not find forcefield for atom C-5 with 0 bonds
Can not find forcefield for atom C-6 with 0 bonds
Can not find forcefield for atom C-7 with 0 bonds
Can not find forcefield for atom C-8 with 0 bonds
Can not find forcefield for atom C-9 with 0 bonds
Can not find forcefield for atom C-10 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 144 atoms

I had not got this error when using  version 3.3.1 with this
particular task. Why does it consider the carbon has zero bonds...?

Any ideas what to do would be gratefully appreciated.

Vitaly