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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Received on Wed Sep 12 2012 - 06:00:07 PDT
