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

[David]

On Thu, 2005-07-14 at 15:44 -0400, Kai Zhuang wrote:
> i solved the problem (i think i did) by cut and paste the ligand and
> receptor into two seperate files, did seperate pdb2gmx, then merged
> the gro files and top files later.
> 
> why does this work?  i didn't make any modification to the structure,
> only pdb2gmx-ed them in parts.
> 
> also, if my topology file is one master.top linking two itp files:
> ligand.itp and receptor.itp, what do i do with the pres.itp generated
> by pdb2gmx? how do i merge them?
> 
what is pres.itp?

> thanx :)
> 
> On 7/13/05, David <spoel at xray.bmc.uu.se> wrote:
> > On Wed, 2005-07-13 at 15:48 -0400, Kai Zhuang wrote:
> > > 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?
> > 
> > I suspect that the pdb file is corrupt, e.g. has tabs instead of spaces.
> > Try viewing it with rasmol or something like that.
> > 
> > >
> > > 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
> > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > >
> > > >
> > >
> > >
> > --
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> > 
> 
> 
-- 
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
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