[gmx-users] bus error / opps, sorry david, sent reply to ur private inbox by accidnet

Kai Zhuang kai.zhuang at gmail.com
Wed Jul 13 21:07:41 CEST 2005

i get an bus error on a mutated ligand/receptor binding system while
doing pdb2gmx.

i have concluded that the problem has nothing to do with my mutation
of the original structure.   i have no idea what's going on, -debug
flag does not result in anything different

the error log shows as this:
Linking CYS-6 SG-41 and CYS-11 SG-74...
Linking CYS-7 SG-47 and CYS-28 SG-220...
Linking CYS-20 SG-152 and CYS-40 SG-310...
There are 75 donors and 77 acceptors
There are 104 hydrogen bonds
Will use HISB for residue 26
Will use HISB for residue 31
Checking for duplicate atoms....
deleting duplicate atom    O  ASN  21 ch A  pdb nr  312
deleting duplicate atom    O  THR  51 ch A  pdb nr  474
Now there are 403 atoms
Bus error

sorry about sending emails to your private inbox,
i didn't realize Gmail's reply function toss mails to private mailbox
instead of the list
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com

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