Re: [AMBER] Uridine diphosphate rhamnose (UDP-Rha)

From: David A Case <>
Date: Wed, 14 Dec 2016 11:16:03 -0500

On Wed, Dec 14, 2016, Imma Speciale wrote:
> I have a problem with the building of UDP-Rhamnose in xleap. I have the pdb
> of the nucleotides, but when I try to put it in Xleap, I obtain error
> messages as show below:

You are correct: "UPG" is not in any of the standard Amber libraries. You
have to create a library yourself. Usual strategies (no real order here):

1. Google something like "UDP-Rhamnose amber force field" to see if anyone
else has done this first. (There are some very good looking hits here; even
if you don't follow them in detail, it's generally a good idea to understand
what others are doing with the same or very similar ligands.)

2. Visit the R.E.D. website:

3. Use antechamber: you will need a pdb file with all hydrogens present, and
then the rest is pretty simple. (Be aware, however, that phosphates create
some special problems: in particular, you probably want to turn of
minimization during the am1-bcc charge derivation). Tutorial B4 at the
Amber web site walks you through this.


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Received on Wed Dec 14 2016 - 08:30:04 PST
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