Hi all,
As usual thank you for your suggestions/help!
Just an additional comments regarding this sentence:
“I think you have to treat this force field as being for RNA only.”
Yes, we are interested to treat this force field as being for RNA only.
We were thinking in performing these steps to reach this goal:
A) to create 4 prepin files, one for each RNA bases with modified atom
types for those atoms that are touched by the new parameters by, for
example adding R at the end: e.g. like H62 -> H62R.
B) create a frcmod files with the new parameters with those “***R”-atom
types.
If you have any additional suggestion about it, just let us know! Thank you!
On Thu, Aug 16, 2018 at 5:57 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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 Sat Aug 18 2018 - 10:00:02 PDT
