Re: [AMBER] RNA's sugar modification

From: Bill Ross <>
Date: Sun, 15 Mar 2015 13:17:57 -0700

PS - I think savemol2 or similar is more up-to-date than saveamberprep.


<div>-------- Original message --------</div><div>From: Bill Ross <> </div><div>Date:03/15/2015 1:13 PM (GMT-08:00) </div><div>To: AMBER Mailing List <> </div><div>Subject: Re: [AMBER] RNA's sugar modification </div><div>
</div>It sounds like you need to make your own residue templates with the modified sugars. For this you need to probably adjust atom types, so reading force field paper(s) would be in order.

You could make a copy of each residue, giving it a suitable name, delete the bond, edit selected atoms to set type, then saveamberprep to save the templates. Then loadpdb with a pdb having the new residue names and the desired conformation. Tutorials should lay this out in more detail.


<div>-------- Original message --------</div><div>From: jacob wick <> </div><div>Date:03/15/2015 11:05 AM (GMT-08:00) </div><div>To: AMBER Mailing List <> </div><div>Subject: [AMBER] RNA's sugar modification </div><div>
</div>Hi all,
I have downloaded a RNA molecule pdb from Nucleic acid databse. When I am
trying to modify its sugar ring in xleap ( as I want to cleave its c2' -
c3' bond), loading it again in leap giving me the unmodified structure back
(I guess leap is adding the modified residues back to the residue
tamplate). Please suggest how can I modify all sugar ring present in the

Thanks in advance,
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Received on Sun Mar 15 2015 - 13:30:03 PDT
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