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
http://amber.ch.ic.ac.uk/doc/leap.txt
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
