AMBER Archive (2008)

Subject: AW: AMBER: tleap and Zn parameter

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Wed Sep 03 2008 - 02:18:28 CDT

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 ZNA
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: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]Im Auftrag
von David A. Case
Gesendet: 02 September 2008 22:41
An: amber_at_scripps.edu
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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