Hi,
Fixed for the upcoming AmberTools 1.3 release.
Thanks for the report Alexander Boncheff.
Thanks for the debugging Mark Williamson.
Scott
On Wed, Nov 04, 2009 at 09:06:53AM -0800, Mark Williamson wrote:
> Alexander Boncheff wrote:
> >So I finally figured out how to debug using gdb.
> >
>
> Nearly, you also need to add debugging symbols by compiling with -g
> >
> >(gdb) run -i /file.pdb -f pdb -o /file.frcmod
> >
> >Starting program: /amber10/bin/parmchk -i /file.pdb -f pdb -o /file.frcmod
> >-p $AMBERHOME/dat/leap/parm/parm99.dat
> >
> >Program received signal SIGSEGV, Segmentation fault.
> >0x0000000000414a26 in rprepi ()
> >(gdb)
> >
>
> Hi Alex,
>
> In a nutshell, you are using this tool incorrectly and it is crashing
> without telling you this. Admittely, parmchk should fail in a nicer manner.
>
>
> Looking at the AmberTools manual
> http://www.lulu.com/items/volume_63/2232000/2232695/2/print/AmberToolsi.pdf
> (p68), you are actually using this tool incorrectly; you should be
> passing it a prepi, ac or mol2 file; not a pdb file
>
>
> For reference, this was debugged using the following method and the
> file.pdb that you sent me offlist:
>
> 1) Change to the correct directory
>
> cd $AMBERHOME/src
>
>
> 2) Add debugging symbols and turn off optimisations within the build
> process.
>
> edit config.h
>
> change:
>
> CFLAGS= -m64 -DBINTRAJ $(AMBERBUILDFLAGS)
> OCFLAGS=-O3 -m64 -DBINTRAJ $(AMBERBUILDFLAGS)
>
>
> to:
>
> CFLAGS= -m64 -DBINTRAJ $(AMBERBUILDFLAGS) -g
> OCFLAGS=-O0 -m64 -DBINTRAJ $(AMBERBUILDFLAGS) -g
>
> 3) Rebuild parmchk
>
> cd $AMBERHOME/src/antechamber
> make clean ; make ; make install
>
> 4) Run parmchk again, but via gdb
>
> cd $AMBERHOME/exe
> gdb ./parmchk
>
> Withing gdb, execute the following command:
>
> run -i file.pdb -f pdb -o file.frcmod
>
> Hopefully this should crash:
>
> (gdb) run -i /tmp/file.pdb -f pdb -o /tmp/frcmod
> Starting program: /server-home/mjw/code/AMBER/amber10/bin/parmchk -i
> /tmp/file.pdb -f pdb -o /tmp/frcmod
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x0000000000414eef in rprepi (filename=0x52cf00 "/tmp/file.pdb",
> atomnum=0x52a5b8, atom=0x52e010, bondnum=0x52a5bc, bond=0x53f820,
> cinfo=0x52db80, minfo=0x52d120) at prep.c:120
> 120 rotate0(atm[tmpint4 - 1],
> atm[tmpint3 - 1],
>
> 5) Run a backtrace
>
> (gdb) bt
> #0 0x0000000000414eef in rprepi (filename=0x52cf00 "/tmp/file.pdb",
> atomnum=0x52a5b8, atom=0x52e010, bondnum=0x52a5bc, bond=0x53f820,
> cinfo=0x52db80, minfo=0x52d120) at prep.c:120
> #1 0x0000000000426b17 in main (argc=7, argv=0x7fbfffee18) at parmchk.c:4063
> (gdb)
>
>
> 6) Locate the regions in the source code reported by gdb:
>
> parmchk.c:4063 is
>
> if (format == 0)
> overflow_flag = rprepi(ifilename, &atomnum, atom,
> &bondnum, bond_array, &cinfo, &minfo); <--
>
> which is calling rprepi() which then segfaults at prep.c:120
>
> This is incorrectly attempting to parse a pdb file as a prepi file; the
> "format" variable in main.c never gets incremented on from 0 when
> processing the value of -f since there is no pdb option here, hence
> rprepi() is called. rprepi() cannot deal with pdb files and as a result,
> crashes.
>
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Received on Mon Dec 14 2009 - 10:30:03 PST
