Dear Imma,
Considering that L-Rhamnose is a 6-deoxy sugar you could construct
UDP-Rhamnose:
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.
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
&
http://q4md-forcefieldtools.org/REDDB/projects/F-85/
You can do the job at: http://q4md-forcefieldtools.org/REDServer-Development/
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
---
http://q4md-forcefieldtools.org/FyD/
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Received on Thu Dec 15 2016 - 10:30:02 PST
