[gmx-users] bus error during pdb2gmx

[Kai Zhuang]

hi,

i am getting a strange bus error while doing pdb2gmx
anyidea what's happening here?  there's no other error log

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



-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
6478314789