On Thu, Feb 11, 2016, kaushik chakraborty wrote:
>
> I was trying to perform qm/mm simulation of a RNA molecule using CHARMM
> forcefield in amber 12. It was running fine when I there is only RNA
> atoms within the QM region. But as I consider one Na+ ion along with
> RNA atoms within the QM region it was showing that "Unable to correctly
> identify element SOD".
The CHARMM code (and force fields) generally eschew all nomenclature standards
in favor of backwards compatibility with their own software. Sometime back in
pre-history, they decided to call sodium "SOD", whereas Amber, the PDB, etc
use "NA".
How did you prepare the prmtop file that has the CHARMM force field: this
might be someting we can fix if the workflow involved parmed; (less likely if
the workflow involved chamber, which we are not continuing to develop.
You might try editing (a copy of) your prmtop file to change "SOD" to "
NA". Also check the values in the "ATOMIC_NUMBER" section to make sure
they are correct.
Aside: if you are using the CHARMM force field for RNA, be sure that it is
a very recent version of their force fields.
...good luck....dac
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Received on Thu Feb 11 2016 - 15:00:03 PST
