AMBER Archive (2006)

Subject: Re: AMBER: Using modified NA bases

From: FyD (fyd_at_u-picardie.fr)
Date: Tue Oct 24 2006 - 13:14:54 CDT


Quoting sethl_at_gatech.edu:

> I would like to know the most common way to go about building nucleic acid
> complexes with custom/modified bases. Right now I have generated a
> library of
> prep files that contain my modified bases but then how would I go about
> constructing a structure file for a helicoidal duplex using these bases?

R.E.D. generates Tripos mol2 files which can be used instead of prep
files in LEaP.
LIB = loadmol2 yourfile.mol2

You can find nucleotide fragments in R.E.DD.B. as examples. See for instance:
Projects: F-61 up to F-64; F-57 up to F-59

regards, Francois

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