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
>
>
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>
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Received on Wed Sep 12 2012 - 23:30:03 PDT
