On Fri, Nov 04, 2016, Anna Cebrian Prats wrote:
> I am working with Uridine diphosphate (UDP) bonded with a sugar and I have
> some problems.
>
> The problem is that the RNA.OLE force field doesn't contain a template
> name to define UDP.
The contributed parameters database has entries for ADP and GDP. I'd
take one of those and modify the base to be U. To a good extent, you
should just be able to swap in the atom types and charges from a regular U
residue into ADP.
Beyond that, it's unclear exactly what you mean by saying that UDP is "bonded"
to a sugar. If this is a covalent bond, then you will have more work to do
to create a complete force field. If it's a non-covalent interaction, once
you get UDP created, you should be fine.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 04 2016 - 10:30:02 PDT
