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

From: FyD <>
Date: Thu, 15 Dec 2016 19:06:29 +0100

Dear Imma,

Considering that L-Rhamnose is a 6-deoxy sugar you could construct
using uridine (nucleoside) + L-Rhamnose (methyl-oside version) + two
phosphate derivatives (the central + the terminal one) thus you could
build also UMP-Rhamnose and UTP-Rhamnose.


You can do the job at:

regards, Francois

> 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:
> FATAL: Atom .R<UPG 2>.A<N1 1> does not have a type.
> FATAL: Atom .R<UPG 2>.A<C2 2> does not have a type.
> FATAL: Atom .R<UPG 2>.A<N3 3> does not have a type
> .....
> I think that the problem is the name, xleap don't recognize the UPG name.
> Thus, I have changed the library (I have tried to use .gaff, .ff10,
> .ff12SB, .ff99SB), but the problem is the same!!
> Can you help me?? Do you know how can I build the correct UDP-rhamnose?

           F.-Y. Dupradeau

AMBER mailing list
Received on Thu Dec 15 2016 - 10:30:02 PST
Custom Search