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

[Kai Zhuang]

anyway you can help me without having the pdb file?
i'm bound by contract with another group to not share the file

can you just give me some ideas on where to look?

On 7/13/05, David <spoel at xray.bmc.uu.se> wrote:
> On Wed, 2005-07-13 at 15:07 -0400, Kai Zhuang wrote:
> > 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
> 
> Plz send me the pdb file.
> >
> > ps.
> > david,
> > 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
> --
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 


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