AMBER Archive (2001)

Subject: Re: Non-standard DNA bases

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jun 13 2001 - 00:29:40 CDT

>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.

Bill Ross