From: Stefan Franzen (Stefan_Franzen_at_ncsu.edu)
Date: Mon Feb 13 2012 - 09:31:12 CST

We are trying to create a patch for nucleotides that consists of both
2'-deoxy and 2'-O methyl ribonucleotides. The default deletes 2'-O methyl
so it appears necessary to develop a patch. However, there must be an
internal patch since the PSF builder automatically puts a second phosphate
into the patch that we added. We need to understand how to design a patch
that is consistent with the internal workings of the PSF builder, but have
no way to do this without knowing the precise way that the PSF builder
works.

-- 
Stefan Franzen
Professor of Chemistry
North Carolina State University
Raleigh, NC 27695
Phone: 919-515-8915