Re: [modeller_usage] NADPH

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 05/25/2011 09:47 AM, flavio seixas wrote:
> I want to modelate a protein wit NADPH bonded. However, my template
> has NADH bonded. Here is parte the alignment file I am using with:
>
> > structure
> CCCCCCCCCCCCC4
>
> > sequence
> BBBBBBBBBBBBB.

That should work, but normally you would use '.' in the structure as
well (not 4). The '.' residue type simply copies a residue from the
structure to your model.

> My question is: Which is the align code for NADPH??

There isn't one, and even if there were, it wouldn't make any
difference. Whatever code you use in the structure is ignored when you
align it with '.' in your model - it's as if you used '.' in the structure.

> If there is no code, how can I replace NADH by NADPH with modeller?

You can't with Modeller - it simply copies ligands from template to 
model. One way to do this outside of Modeller is to change NADH to NADPH 
in your template file, either by manually editing the PDB file to add 
the phosphate or by using another piece of software that can do it.

	Ben Webb, Modeller Caretaker
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