Re: [modeller_usage] Nucleic Acids and modeller

[Modeller Caretaker <>]

On Fri, Jun 25, 2004 at 05:19:44PM -0500, Luis Rosales wrote:
> I need to model a protein complexed to a nucleic acid...
> I know my alignment should look like:
> PROTEIN/NUCLEIC-ACID
> But I was wondering if I should define new libraries in my top file

There shouldn't be any need to do that. If you look in
modlib/top_heav.lib (for example - that's for the heavy-atom topology)
you should find defined topologies for your standard nucleic acids (i.e.
URA, THY, GUA, CYT, ADE residue types).

> and how do you tell modeller:
> "Hey, this is a nucleic acid, A stands for adenine!!" (I will be working
> with poly Uracil...)

These residues are also listed in modlib/restyp.lib. You simply need to
change the 1-letter code for each nucleic acid (currently '#' for every
one) to something more useful, and then use the codes you chose there in
your alignment file. (Obviously you can't use 'A' for adenine though as
it is already used to represent alanine, for example.)

	Ben Webb, Modeller Caretaker
-- 
             http://www.salilab.org/modeller/
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