[gmx-users] bus error / opps, sorry david, sent reply to ur private inbox by accidnet
spoel at xray.bmc.uu.se
Wed Jul 13 21:39:34 CEST 2005
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.
> 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 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
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