AMBER Archive (2005)

Subject: Re: AMBER: leap question

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Fri Aug 05 2005 - 20:56:40 CDT

On Aug 5, 2005, at 3:34 PM, David A. Case wrote:

> On Fri, Aug 05, 2005, Kara Di Giorgio wrote:
>
>> Created a new atom named: C4 within residue: .R<Ni 13>
>
> As Amber error messages go, this is pretty specific: the pdb file
> appears to
> have an atom named "C4" in a residue named "Ni". You will have to
> hand-edit
> your pdb file to get atom C4 to be in residue NCH (I assume).

There is no residue named Ni in the pdb used. This was one reason I
was confused.

This is the procedure I used to assemble my model:
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,
added the Ni bonds and saved it as NCH.
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).

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?

I do understand about renaming the pdb file to exactly match the unit
in leap and have gotten it to work with a different unit and this pdb
for the DNA without a hitch. That unit was a single unit created in
antechamber (no merge afterward).

I guess my main question is, how do you rename a new unit (made up of
other units) and use that new name in a later step?

Thank you for your help,

Kara Di Giorgio

p.s. I'll try to make my questions more clear in the future.

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