[gmx-users] x2top stalls when generating topology file

Robert Johnson bobjohnson1981 at gmail.com
Wed Jun 27 19:08:26 CEST 2007

Hello everyone,
I asked this question in the past without a response, so I'll give it
another shot.

There have been other reports on the mailing list where users attempt
to generate
a topology with x2top only to have the program stall and generate no output. I'm
using x2top (from Gromacs version 3.3.1) to generate topology files for infinite
carbon nanotubes and graphene sheets. Starting from a pdb file with box
dimensions compatible with PBC I enter:

x2top -f <coordinates>.pdb -o <topology>.top -pbc

I then select force field 7 (the deprecated Gromacs force field) and I get the
following output:

Looking whether force field file ffgmx.rtp exists
Opening library file /home/bob/programs/gromacs/share/gromacs/top/ffgmx.rtp
Generating bonds from distances...
Opening library file /home/bob/programs/gromacs/share/gromacs/top/ffgmx.atp
There are 53 type to mass translations
atom 0

At this point the program just sits there while still occupying 100% of the CPU.
I don't experience this problem when using x2top from version 3.3 that was
compiled on a different machine. Does anyone know the fix to this problem?
Maybe it has to do with the way the code is compiled?

I'd like to also note that I also observe these stalls when using genion.

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