On Tue, Aug 30, 2011, Indrajit Deb wrote:
> I want to prepare single nucleotide. I mean phosphate at the C5'-end and
> base at C1'. In the all_nuc94.in file RU5, RU3 etc are given, but the
> problem is that in case of RU3 how to add OH group with the PO2 group at the
> 5'-end to close the chain and make it a nucleotide. In case of RU5 how to
> add H at the C3'-end to close the chain and make it nucleoside.
>
> I am waiting for helpful suggestions.
First, I suggest you move to ff10.
If you want a nucleoside, use "UN" ("RUN" in the old nomenclature scheme.)
If you want a nucleotide, do the following:
loadAmberPrep nucleic10.in (needed since OHE is here, but not in
nucleic10.lib...needs fixing)
x = sequence { OHE U3 }
The "x" should be the nucleotide you want.
(Also to fix: the above should be in the Users' Manual...}
...hope this helps....dac
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Received on Tue Aug 30 2011 - 13:30:02 PDT
