AMBER Archive (2006)

Subject: Re: AMBER: chirality.c line 121

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 27 2006 - 16:46:21 CST

On Wed, Dec 27, 2006, Seth Lilavivat wrote:
>
> While attempting to load some prep files and launch xleap, I get the following
> error:
>
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 121
> !FATAL: Message: Atom P is not in the first list
> !
> !ABORTING.
>
> I changed atom types of the O2' in the prep residues which caused the error. I
> noticed one other similar posting from the mail archives suggesting that a
> bugfix should be applied. Can someone confirm if the error that I have received
> applies to this?

It looks(?) like you are still using Amber 8, and have not applied bugfix.15.
If this is correct, you should certainly apply that patch (and the others).
That will improve the error message, which should make it easier to track down
the source of the problem -- which arises from the way the connect atoms are
specified in user-created residues.

Unfortunately, as you have found out, the way in which connect atoms are
processed is not well documented. You might try to ask the people at Georgia
(see http://www.glycam.com/index.jsp), since they have the most experience
in dealing with unusual connection patterns.

An alternative is just to stick in a TER card before or after your modified
residue, than use the "bond" command in LEap to create the connection.

...good luck...dac

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