On Mon, Sep 21, 2015, Robert Molt wrote:
>
> 1.) In tutorial5, the authors list several main chain atoms.
>
> However, the manual states, on p.275, "By default, the program generates
> a mainchain itself. However, you may also specify the main-chain atoms
> in the main chain file..." through to the end of the top of p.276.
>
> I am confused: it says the program generates the mainchain
> automatically. Either my interpretation of the manual is flawed or the
> tutorial was just writing this for the fun of it?
Did you try using the prepgen defaults? The tutorial says that one
"generally" needs to identify the mainchain atoms manually. My recollection
is that relying on prepgen might work if you have just a modified side chain,
but won't work where the backbone itself is modified (as in this case).
But don't rely on my recollection: experimenting with what happens, (and even
studying the code) is the best way to learn.
>
> 3.) I would assume that, if a PDB DNA strand is written 5' to 3', the
> "head" will be defined as oxygen ester nearest the methylene outside the
> ribose (and the tail is thus what was the ribose alcoholic oxygen before
> dehydration synthesis)? This is my understanding of biochemistry, but
> perhaps I do not know if the implicit terminal caps of leap DNA strands
> somehow change what is my perception of how this works.
Use the ever-helpful "desc" command in tleap to see how head and tail
atoms in standard nucleotides are identified. Generally, the head atom
will be "P" and the tail atom will be "O3'".
....dac
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Received on Tue Sep 22 2015 - 05:30:03 PDT
