AMBER Archive (2008)

Subject: Re: AMBER: building quadruplex with nab

From: David A. Case (case_at_scripps.edu)
Date: Wed May 21 2008 - 00:08:10 CDT

On Tue, May 20, 2008, Rabin wrote:

> I want to do some editing of pdb file with nab. I want to remove a
> nucleotide from the loop with four nucleotide and also replace a nucleotide
> with another nucleotide in the loop. Is removing or editing of nucleotide
> possible with nab? can someone give me the way to do this?

You can look at the "Molecule Creation Functions" and "Create Biomolecules"
section of the Users' Manual. In this case, however, it is generally simpler
to edit the pdb file to get what you want, then use getpdb() to load it into
NAB.

...good luck...dac

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