[gmx-users] x2top hangs up

Vitaly Chaban chaban at univer.kharkov.ua
Sun Sep 14 16:03:14 CEST 2008


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

What essential things have been changed in x2top since 3.3.1?

Thanks a lot for suggestions!

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban

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