[AMBER] Uridine diphosphate (UDP) - tleap

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From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
Date: Fri, 4 Nov 2016 11:58:51 +0000

Hi amber users.

I am working with Uridine diphosphate (UDP) bonded with a sugar and I have some problems.

First of all, I am using xleap or tleap to source the Glycam force field in order to define my sugar.

Then, I sourced the RNA.OL3 force field to define the UDP group.

The problem is that the RNA.OLE force field doesn't contain a template name to define UDP.

So, how can I define the diphosphate or the extra phosphate?

I added my pdb file.

Thank you for your help in advanced

Anna

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Received on Fri Nov 04 2016 - 05:00:03 PDT