On Wed, Sep 16, 2015, Robert Molt wrote:
>
> I am confused on proper parameterization of units which are covalently
> bound. I am going to introduce a modified nucleotide into a DNA crystal
> structure of a standard helix properties. I thus need to create a unit
> in leap to identify the modified nucleotide. My question is independent
> of the nature of modified nucleotide, so I will just frame them in terms
> of adenine.
>
> In adenine nucleotide, I would inherently put a hydroxyl group on the
> ribose for parameterization. An internal ribose would actually have this
> be a linkage to the next phosphate. I am confused how this will be read
> properly by leap. When I go to parameterize, it will create a unit with
> for parameters for OH bonds, but the unit I load into leap must discard
> these parameters? Same logic applies for the OH on the phosphate, which
> will in reality make a phosphodiester linkage?
The extra atoms (e.g. a hydroxyl hydrogen) that you add on for the purposes of
parameterization need to be stripped away before LEaP ever sees the new unit.
[This complements my earlier discussions about how "dumb" a program LEaP is:
it doesn't do anything but match atoms in libraries vs pdb file.]
You can use the residuegen program to manually mark the atoms that need to
be stripped away (and then get them removed), or use the prepgen program
with the "-m" option, as in tutorial B5. The former is a little simpler,
and the latter a little more flexible.
....dac
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Received on Wed Sep 16 2015 - 19:30:03 PDT
