On Thu, Aug 14, 2014, Valentina Romano wrote:
>
> I am working with a complex of a kinase bound to ATP and 2 Mg2+ ions.
> >From the .pdb file of this complex, I saved the pdb file of the ATP only.
> I wanted to convert the ATP.pdb into a mol2 file with Antechamnber.
> I got the following error:
>
> Running: /import/bc2/home/schwede/romanov/amber12/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> For atom[6]:PB, the best APS is not zero, bonds involved by this atom are frozen
>
> For atom[10]:PA, the best APS is not zero, bonds involved by this atom are frozen
>
> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic double)Error: cannot run "/import/bc2/home/schwede/romanov/amber12/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit
>
> Can anyone help me to understand what happened?
This sounds like a bad geometry (or other problems) with the ATP.pdb file.
Did you use the acdoctor program to look for problems? Error messages in
antechamber can be obscure, but acdoctor is often better. If you can't figure
it out, we would need to see the input PDB file (be sure it has all
hydrogens).
...dac
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Received on Thu Aug 14 2014 - 09:00:02 PDT
