[gmx-users] x2top stalls when generating topology file

[David van der Spoel]

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.
________________________________________________________________________
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
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