[gmx-users] bus error during pdb2gmx

[David]

On Tue, 2005-07-12 at 17:01 -0400, Kai Zhuang wrote:
> hi,
> 
> i am getting a strange bus error while doing pdb2gmx
> anyidea what's happening here?  there's no other error log
> 

try running with the -debug flag

Which gmx-version, which hardware?



> thanks :)
> 
> 
> Back Off! I just backed up posre_W.itp to ./#posre_W.itp.1#
> Processing chain 2 'A' (406 atoms, 51 residues)
> Opening library file /usr/local/gromacs/share/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> Special Atom Distance matrix:
>                     CYS6    CYS7    HIS8   CYS11   CYS20   CYS28
>                     SG43    SG49   NE259    SG79   SG157   SG224
>     CYS7    SG49   0.494
>     HIS8   NE259   1.260   1.085
>    CYS11    SG79   0.204   0.667   1.257
>    CYS20   SG157   1.089   1.342   2.281   1.164
>    CYS28   SG224   0.454   0.205   1.161   0.618   1.338
>    CYS40   SG314   1.091   1.295   2.290   1.192   0.203   1.279
> Linking CYS-6 SG-43 and CYS-11 SG-79...
> Linking CYS-7 SG-49 and CYS-28 SG-224...
> Linking CYS-20 SG-157 and CYS-40 SG-314...
> There are 76 donors and 74 acceptors
> There are 99 hydrogen bonds
> Will use HISB for residue 8
> Checking for duplicate atoms....
> Bus error
> 
> 
> 
-- 
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://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++