[gmx-users] x2top stalls when generating topology file

David van der Spoel spoel at xray.bmc.uu.se
Wed Jun 27 19:22:36 CEST 2007

Robert Johnson wrote:
> 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.
> Thanks,
> Bob
could it be due to the infamous gcc 4.1.x ? A workaround to some of 
these problems is in CVS.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list