My suggestion is to upgrade to AmberTools 12 and use antechamber from
there. If you are still having problems, it'll be easier to help.
(segfaults are hard to diagnose in our own programs, let alone such a
complicated one as mopac that we don't actually develop and haven't used in
years).
HTH,
Jason
On Thu, Sep 13, 2012 at 2:03 AM, Anogna <anognal.gmail.com> wrote:
> Dear David,
>
> I tried to regenerate the mol2 file using -nc flag
>
> I used:
> antechamber -i lgn_h.pdb -fi pdb -o lgn.mol2 -fo mol2 -c bcc -nc 1 -j 5
>
> Error was:
>
> Total number of electrons: 72; net charge: 1
>
> Running: /applications/smp/amber/10/intelmpi-mkl/bin/mopac.sh
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> mopac 40000000000FA490 Unknown Unknown Unknown
> mopac 4000000000101900 Unknown Unknown Unknown
> mopac 4000000000044A30 Unknown Unknown Unknown
> mopac 40000000000B5870 Unknown Unknown Unknown
> mopac 40000000000141F0 Unknown Unknown Unknown
> mopac 4000000000003350 Unknown Unknown Unknown
> libc.so.6.1 2000000000407D60 Unknown Unknown Unknown
> mopac 4000000000003180 Unknown Unknown Unknown
> Error: unable to find mopac charges in mopac.out
>
> Can u plz help me out of this.
>
>
> Regards,
> Anogna
>
> On Wed, Sep 12, 2012 at 6:18 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Wed, Sep 12, 2012, Anogna wrote:
> > >
> > > I tried to convert my ligand pdb file to Mol2 file using antechamber.
> > >
> > > Total number of electrons: 79; net charge: 0
> > > INFO: Number of electrons is odd: 79
> > > Please check the total charge (-nc flag) and spin multiplicity
> (-m
> > > flag)
> >
> > Antechamber can only deal with closed-shell molecules with an even number
> > of
> > electrons. Check your pdb file to make sure it is correct (with all
> > hydrogens
> > present in good locations). If the molecule has a charge other than
> zero,
> > you
> > have to use the "-nc" flag.
> >
> > >
> > > Running: /applications/smp/amber/10/intelmpi-mkl/bin/mopac.sh
> > > *** glibc detected ***
> /applications/smp/amber/10/intelmpi-mkl/bin/mopac:
> > > malloc(): memory corruption: 0x60000000046fc1a0 ***
> > > ======= Backtrace: =========
> > > /lib/libc.so.6.1[0x20000000004af090]
> >
> > Make sure the test cases pass: it looks like you might have a
> > non-functional
> > version of mopac. Consider upgrading AmberTools to a more current
> version.
> >
> > ...good luck....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ...........INDIA is great
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 13 2012 - 05:00:04 PDT
