[gmx-users] x2top hangs up

[David van der Spoel]

Vitaly Chaban wrote:
> Hello,
> 
> Trying to generate a topology from PDB file my x2top (gromacs 4.0beta) hangs up.
> I have the coordinates of carbon nanotube in the PDB file (generated
> with MOLEKEL). I also have
> 
> ffencadv.n2t with:
> C C 1 C ; CNT Carbon with one bond
> C C 2 C C ; CNT double bonded Carbon
> 
> ===============================
> ffgmxbon.itp with:
> [ bondtypes ]
> ; i j func b0 kb
> C C 1 0.14210 478900.
> [ angletypes ]
> ; i j k func th0 cth
> C C C 1 120.000 397.480
> [ dihedraltypes ]
> ; i l func q0 cq
> C C 1 0.000 167.360
> 
> x2top -f cnt.pdb -o cnt.top -ff select
> Then I select  "8: Encad all-atom force field, using scaled-down vacuum charges"
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.rtp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.n2t
> Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.n2t
> There are 0 name to type translations
> Generating bonds from distances...
> atom 0
> 
> And the programme hangs up. The processor load is 99% all the time
> before I terminate the job.
> 
> The same data input works with GROMACS 3.3.1 as described by C. Stiles
> but not with 3.3.3 and 4.0b however.
> If it is not a bug then what should be modified to make a topology?
> Has anyone tried to make SWCNT topology in the versions newer that
> 3.3.1?
> 
> What essential things have been changed in x2top since 3.3.1?
> 
> Thanks a lot for suggestions!
> 
The 3.3.3 and 4.0 versions are the same. Since I am busy completely 
reworking the code you can consider the current version broken. The 
topology from 3.3.1 will still work though...

-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se