On Mon, Dec 17, 2012, Asmita Gupta wrote:
>
> It is usually suggested that while preparing a nucleic acid system for
> simulation, 5' terminal phosphate group must be removed; or any terminal
> charged phosphate group should be removed...
>
> Can you please explain why it should be like that??
The most common synthetic approach to creating oligonucleotides has a 5'
group with no phosphate, so the default 5' library in Amber follows this idea.
If you wish to have the 5' phosphate there, modify your leaprc file so that
the first residue in each chain will be an ordinary nucleotide (e.g. "G", not
"G5"). You can use the OHE group to "cap" the 5' residue, that is, your
sequence could be { OHE G C U .... }.
You should be aware, however, that this procedure is not well tested. The
charges on the 5' phosphate group are those appropriate for a phosphate in the
middle of the chain, not the end. Also, this procedure will yield a
protonated phosphate, which may not be what you want. If the presence and
behavior of the 5' phosphate is important, you will need to develop parameters
for a new terminal residue that more closely matches what you want.
...dac
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Received on Mon Dec 17 2012 - 05:30:04 PST
