Hi
The following is my ligand pdb file
REMARK Created: Thu Sep 13 11:10:12 India Standard Time 2012
HETATM 8833 C1 COM A 1 19.831 16.769 69.471 1.00 0.00
C
HETATM 8834 C2 COM A 1 20.941 17.638 69.469 1.00 0.00
C
HETATM 8835 C3 COM A 1 19.620 15.877 68.404 1.00 0.00
C
HETATM 8836 C4 COM A 1 21.863 17.622 68.383 1.00 0.00
C
HETATM 8837 C5 COM A 1 20.523 15.850 67.326 1.00 0.00
C
HETATM 8838 C6 COM A 1 21.633 16.717 67.318 1.00 0.00
C
HETATM 8839 C7 COM A 1 23.070 18.532 68.329 1.00 0.00
C
HETATM 8840 O8 COM A 1 24.030 18.214 67.593 1.00 0.00
O
HETATM 8841 O9 COM A 1 21.089 18.480 70.534 1.00 0.00
O
HETATM 8842 N10 COM A 1 20.326 15.002 66.307 1.00 0.00
N
HETATM 8843 O17 COM A 1 23.087 19.579 69.016 1.00 0.00
O
TER
END
can u plz verify if and suggest me is any problem in my pdb file that
causing me the error as I mentioned in my previous msg.
On Thu, Sep 13, 2012 at 5:17 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 13 2012 - 22:30:02 PDT
