Re: Non-standard DNA bases

From: David Konerding <>
Date: Wed 13 Jun 2001 07:41:09 -0700

Bill Ross writes:
> >You could consider using leap to set torsion angles -
> >see the alpha/beta protein config file. It seems like
> >it'd be a lot easier.
>It has been pointed out to me that leap's impose cmd
>has a problem with cyclic situations such as nucleic
>acid sugars. It may be possible to work around this
>by using residues defined with a sugar bond missing,
>saving pd, and reloading, converting to real residues
>with pdbResMap.

Presuming there's no huge difference between the modified
residue and a standard base, I would just generate the initial
nucleic acid using nucgen using standard bases, then modify them by
hand in the PDB file, then load them into LEaP using pdbResMap
to convert them. I don't think anybody has actually put effort into
making nucgen work with other bases-- although I believe it's "simply"
a matter of generating cylindrical coordinates for the atoms.

Perhaps NAB (nucleic acid builder) has more functionality for working
with non-standard bases?
Received on Wed Jun 13 2001 - 07:41:09 PDT
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