[gmx-users] x2top problem

[Patricia Gómez]

Dear all,

I have a problem in the generation of the topology file of a ligand
using x2top program. I think that it's a problem with
the detection of the connectivity by the program.I am
using the version 3.3.2 of Gromacs.

As an example  i have take only a fragment of my molecule,
that it's a benzamidine group.

ATOM      1  C   ABK     0      -1.230  -1.842   0.078
C
ATOM      2  C   ABK     0      -0.039   0.308   0.150
C
ATOM      3  C   ABK     0       0.010  -2.531   0.093
C
ATOM      4  C   ABK     0       1.225  -1.801   0.134
C
ATOM      5  C   ABK     0       1.200  -0.384   0.164
C
ATOM      6  C   ABK     0      -0.046   2.022   0.175
C
ATOM      7  C   ABK     0      -1.254  -0.424   0.102
C
ATOM      8  H   ABK     0      -2.193  -2.420   0.045
H
ATOM      9  H   ABK     0       0.029  -3.654   0.071
H
ATOM     10  H   ABK     0      -1.494   2.171   1.516
H
ATOM     11  H   ABK     0      -0.807   3.690   0.913
H
ATOM     12  H   ABK     0       1.997   2.551  -0.694
H
ATOM     13  H   ABK     0       0.660   3.385  -1.519
H
ATOM     14  H   ABK     0       2.163   0.193   0.197
H
ATOM     15  H   ABK     0       2.208  -2.346   0.142
H
ATOM     16  H   ABK     0      -2.237   0.119   0.084
H
ATOM     17  N   ABK     0      -0.826   2.661   0.908
N
ATOM     18  N   ABK     0       0.999   2.793  -0.751
N
CONECT    7    1    2   16
CONECT    1    7    3    8
CONECT    2    7    5    6
CONECT    3    1    4    9
CONECT    4    3    5   15
CONECT    5    2    4   14
CONECT    6    2   17   18
CONECT   17    6   10   11
CONECT   18    6   12   13

when i run x2top program i obtained:

 WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file
/software2/gromacs-3.3.2/exe/share/gromacs/top/aminoacids.dat

Opening library file /software2/gromacs-3.3.2
/exe/share/gromacs/top/atommass.dat
Opening library file /software2/gromacs-3.3.2
/exe/share/gromacs/top/vdwradii.dat
Opening library file /software2/gromacs-3.3.2/exe/share/gromacs/top/dgsolv.dat

#Entries in atommass.dat: 83 vdwradii.dat: 27 dgsolv.dat: 7
Looking whether force field files exist
Opening library file /software2/gromacs-3.3.2
/exe/share/gromacs/top/ffoplsaa.rtp
Opening library file ffoplsaa.n2t
WARNING: all CONECT records are ignored
Opening library file ffoplsaa.n2t
There are 21 name to type translations
Generating bonds from distances...
atom 18
Can not find forcefield for atom C-2 with 2 bonds
Can not find forcefield for atom C-6 with 1 bonds
Can not find forcefield for atom N-17 with 2 bonds
Can not find forcefield for atom N-18 with 3 bonds

-------------------------------------------------------
Program x2top, VERSION 3.3.2
Source code file: x2top.c, line: 206

Fatal error:
Could only find a forcefield type for 14 out of 18 atoms


I know that i can add these atoms to the ffoplsaa.n2t file. But what i
don't understand is that the program says that C6 atom is attached by 1
bond, whereas
in fact it's attached to 3 atoms. C2 has 3 bonds (not 2) and N17 has 3 bonds
(not 2).
I tried to include the atoms in the ffoplsaa.n2t but i must did it in the
wong connectivity.

Thanks in avance for your help and best regards,

Patricia
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