Re: [AMBER] Uridine diphosphate (UDP) - tleap

From: David A Case <>
Date: Fri, 4 Nov 2016 13:07:21 -0400

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

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Received on Fri Nov 04 2016 - 10:30:02 PDT
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