[gmx-users] x2top hangs

[Scott Milner]

Folks -- I cannot manage to get x2top to work on even the simplest  
example.
Here is "ethane.pdb", a PDB file for ethane (built using Avogadro,  
with the CONECT records stripped out):

COMPND    UNNAMED
AUTHOR    GENERATED BY OPEN BABEL 2.2.2b1
ATOM      1  C   LIG     1      -3.466  -1.641  -0.001  1.00   
0.00           C
ATOM      2  C   LIG     1      -1.954  -1.689   0.025  1.00   
0.00           C
ATOM      3  H   LIG     1      -3.817  -0.605   0.026  1.00   
0.00           H
ATOM      4  H   LIG     1      -3.882  -2.168   0.863  1.00   
0.00           H
ATOM      5  H   LIG     1      -3.850  -2.112  -0.910  1.00   
0.00           H
ATOM      6  H   LIG     1      -1.570  -1.218   0.934  1.00   
0.00           H
ATOM      7  H   LIG     1      -1.538  -1.163  -0.839  1.00   
0.00           H
ATOM      8  H   LIG     1      -1.603  -2.726  -0.002  1.00   
0.00           H
END


I try to run the following command under GROMACS 4.0,

x2top -f ethane.pdb -o ethane.top

with the most recent version of the file ffoplsaa.n2t in its proper  
place (/usr/local/gromacs/share/gromacs/top/),
and I get the following output:

...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
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 /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Looking whether force field files exist
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t
There are 23 name to type translations
Generating bonds from distances...
atom 0

... and then the program hangs.

Can someone confirm that x2top actually works, and send a simple  
working example to me?


Scott Milner
William H. Joyce Professor
The Pennsylvania State University
Department of Chemical Engineering
120 Fenske Laboratory
University Park, PA 16802
(814) 863-9355
smilner at engr.psu.edu