AMBER Archive (2005)

Subject: Re: AMBER: leap question

From: David A. Case (case_at_scripps.edu)
Date: Sat Aug 06 2005 - 06:33:44 CDT

On Fri, Aug 05, 2005, Kara Di Giorgio wrote:

>
> There is no residue named Ni in the pdb used.

OK...I am sorry if I misunderstood the problem.

> 1. I made a CR unit by creating the "crown" portion in antechamber,
> loading it into xLeap and saving it as a unit. I created a unit called
> Ni and saved it. I loaded a pdb with the CR and the Ni, merging them,
                                                          ^^^^^^^^^^^^^

This is not so clear: what exactly to you mean by "merging them"? Did you use
the "combine" command?

> 2. I then loaded a pdb for a piece of DNA with two of the atoms from
> NCH (the CR portion) in it (labeled as the correct atom names and
> residue name NCH).

This is an aside, but if you only have two atoms in the pdb file from
this residue this is unlikely to work well. LEaP can occasionally add a few
missing atoms, but it is not well suited to dealing with a lot of missing
atoms.

>
> I'm wondering if, when I made the NCH from the two portions and then
> saved it, did it not re-name the entire unit? Or is it still named as
> if it's made up of the smaller units? Which name/names would I use in
> my pdb?

Use the "desc" command in LEaP to see exactly what residue names and atom
names you have in your units.

...dac

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