On Thu, Aug 16, 2018, Antonio Amber Carlesso wrote:
>
> We are trying to implement the revised Tan, Piana, Dirks and Shaw RNA force
> field in Amber
>
> *1. **Do the charges in the article table correspond to “Atom name”
> column or “atom type” in the .lib column?*
They are certainly atom names.
> *2. **Is the atom type between RNA and DNA redundant? If yes, do you
> have any idea how to distinguish between RNA and DNA?*
I think you have to treat this force field as being for RNA only.
Stated another way, figuring out how to simulate a mixed DNA/RNA system
with the Tan et al. RNA parameters would represent a major challenge.
....good luck....dac
p.s. don't forget to specify in your leaprc file the water and ion model
to be using. At a glance, the paper seems to use the TIP4P-D water
model and the CHARMM22 force field for ions. Hence, you will need to
make new Amber-format files for these species as well.
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Received on Thu Aug 16 2018 - 09:00:04 PDT
