AMBER Archive (2008)

Subject: RE: AMBER: tleap and Zn parameter

From: Ross Walker (
Date: Wed Sep 03 2008 - 10:31:26 CDT

Hi Susanne,

This is a clear example of where it would save everybody a lot of time if
you were clear about exactly what you were trying to do from the beginning.
Posting the link to the example you are following would help everybody and
it creates a link trail. Since this is how all modern search engines work so
people would be able to link these message threads together later on.

I assume you are referring to this thread:

I can't see anything wrong with the example here, it clearly states:

"Now, for a protein containing Zn2+ you would edit the PDB and change the
residue name for the zinc atom to ZNA."

Note there is a distinct difference between atom name, residue name and atom

I would encourage you to make sure you understand exactly what is going on
in this example and where the information flow goes with respect to residue
name, atom name, atom type and parameters. Doing this means that you
appreciate what the actual steps involved in creating your own unit etc are.
Once you understand this repeating it for any generic residue of your
choosing should be easy.

All the best

> -----Original Message-----
> From: [] On Behalf
> Of Aust, Susanne
> Sent: Wednesday, September 03, 2008 12:18 AM
> To:
> Subject: AW: AMBER: tleap and Zn parameter
> Hello David,
> now it works! Thank you very much for your help.
> The problem was, that I load two Zinc atoms (zn and ZNA) with my ZNA.lib.
> This comes from a little mistake in the answer from Ross (Amber Archive:
> how
> to prepare Zn.lib, Dec 10 2004)
> Here Ross wrote, that I must load zinc.pdb (ZNA=loadpdb "zinc.pdb"),edit
> and then change in the table the atomtype and the charge, but he also
> change
> the unit name from ZNA to Zn. After that, there exist to unit names for
> zinc.
> But I'm happy, that is know everything ist fine and my amber dynamics
> runs.
> Best regard!
> Susanne
> -----Ursprüngliche Nachricht-----
> Von: []Im Auftrag
> von David A. Case
> Gesendet: 02 September 2008 22:41
> An:
> Betreff: Re: AMBER: tleap and Zn parameter
> On Tue, Sep 02, 2008, Aust, Susanne wrote:
> > Thank you very much for your answer and sorry for my to short error
> > description.
> > Here comes a more detailed error message:
> > when I use desc zn, then is the following output:
> > UNIT name:
> this is bad: there is no unit name. Try "desc K+" to see the expected
> output for a metal ion.
> > Head atom: null
> > Tail atom: null
> > Contents:
> > R<ZNA 363>
> This is weird as well: why would leap think this was resdiue 363?
> One thing you have not done is to give the *complete* list of commands
> you used, and the output it provided. The simplest is to load tleap
> with no leaprc file, the use loadoff to load in the library file, then
> use the desc command.
> >
> > I think, here is the mistake, the ZNA.lib is not completly imported.
> > I proved the pdb, here is ZNA as atomtype and it is the correct numer
> > (363)and also in correct columns, but the ZNA.lib is a little bit
> longer.
> This is confusing: what do you mean by the statement "the ZNA.lib is a
> little bit longer"? Also, it would be much better to post your pdb file
> (with just one residue, ZNA), than to state that you "proved" it.
> Here's my suggestion: just for a test, change the zinc atom to a sodium
> or potassium ion in the pdb file. See if you can load the coordinates
> (Na+) is a standard ion. Then try to see what is different when you use
> the ZNA library.
> ...dac
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