Re: AMBER: Adding residues to a DNA sequence

From: Kara Di Giorgio <>
Date: Fri, 29 Jul 2005 09:39:43 -0700

I've looked at the NAB documentation and I'm not sure I'm up to it.
I've tried the following:

1. making a cgc residue that adds a cg and overlaps the first c in my
sequence using nucgen. Loading this into xLeap and making it a
residue. Re-naming the atoms in the overlap c the same, unique,
numbers as I rename the overlap c in my pdb file. Change the residue
name in the pdb file to match the cgc residue in xLeap and then load
the pdb in xLeap. This doesn't work. It creates a structure that's
all over the place.

2. Try to visually align the molecules in VMD with the hope of saving
the coordinates of the both structures together once I get it
organized. I'm having trouble with the alignment. It's hard using the
mouse to translate and rotate one structure on top of another.

Is there a command to choose atoms of each molecule and "'superimpose"
them in VMD? (I saw that that's available in NAB and it's possible in
Spartan, but I can't figure out how to merge the structures in


Kara Di Giorgio

On Jul 27, 2005, at 2:31 PM, David A. Case wrote:

> On Mon, Jul 25, 2005, Kara Di Giorgio wrote:
>> How do you suggest superimposing the residues? What program would you
>> suggest using? How do I replace the two residues with the longer
>> regular helix. I had thought of this but didn't know how to do it.
> Well, *I* would use NAB (, but there are
> lots
> of programs that can superimpose parts of molecules on top of one
> another,
> often in a visual fashion (e.g. in VMD) so that you can see
> immediately if
> it did what you want or not.
> ...dac
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Received on Fri Jul 29 2005 - 17:52:59 PDT
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