Dear Amber users
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?
Thank you
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
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Received on Thu Aug 14 2014 - 03:00:02 PDT
