Re: Non-standard DNA bases

From: Bill Ross <>
Date: Tue 12 Jun 2001 14:39:05 -0700 (PDT)

                We would be interested in opinions on the best way to build
        DNA duplexes with one or more unusual bases (for example,
        3-nitropyrrole). Especially, is there anything particularly tricky
        about modifying Nucgen so that it takes more than four bases?
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.

Eg in
look for "impose unit seqlist internals"

> mymol = sequence { R1 R2 .. }
> impose mymol ...

And see amber6/dat/leap/cmd/protein.cmd for consraints that
the impose cmd can use w/ proteins.

Bill Ross
Received on Tue Jun 12 2001 - 14:39:05 PDT
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