Hi Elisa,
If you take a look at the leap.RNA.OL3 file, you can read that there is no
'URA' residue name unless you modify lines 97-100.
'DU' would be specific to DNA, and not specified in this file (nor anywhere
else).
You can simply use C, A, G, and U for RNA, or the R prefix: RU, RC, RA, RG.
Hope this helps,
Christina
On Wed, Apr 4, 2018 at 7:05 AM, Elisa FREZZA <elisa.frezza.gmail.com> wrote:
> Dear All,
>
> I would like to use tleap to prepare the topology for a simulation of a
> double-stranded RNA, but it does not recognize the uracil ('Creating new
> UNIT for residue').
>
> I tried to do source leaprc.RNA.OL3 and to change the name of the uracil
> into URA or DU in the pub file.
>
> Thank you in advance
>
> Best,
>
> Elisa
>
> --
> Elisa Frezza, Ph.D.
>
> Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS
> Université Paris Descartes, Faculté de Pharmacie de Paris
> 4 Avenue de l'Observatoire, 75006 Paris
> elisa.frezza.parisdescartes.fr
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>
--
--------------------------------------------------------------
Christina Bergonzo
Research Chemist
NIST/IBBR NRC Postdoctoral Researcher
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Received on Wed Apr 04 2018 - 06:00:04 PDT
