Re: [modeller_usage] How to incorporate NAD and water in my model

[Modeller Caretaker <>]

Charlie Allerston wrote:
> Do you have to use the modeller alignment script?  I have been using ebi 
> software to create a .pir file.

No, you do not need to use Modeller to make your alignment file. 
However, since there are no standard one-letter codes for ligands, you 
will likely have to edit your original alignment in a text editor to put 
in the ligands.

> After reading the modeller files and tutorials i am still at a loss as to 
> how to use these 'blk' characters.  I am trying to get a molecule of fad 
> that is present in my template into my model.

Please go through the advanced tutorial, and if you have a specific 
question, ask it. You could also post your input files. Otherwise, I can 
only give reiterate what's in the documentation, since I don't know what 
your stumbling block is.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage