AMBER Archive (2006)

Subject: Re: AMBER: LEAP error

From: David A. Case (
Date: Sun Oct 08 2006 - 23:28:36 CDT

On Fri, Oct 06, 2006, Akshay Patny wrote:

> > try = loadpdb try2.pdb
> Loading PDB file: ./try2.pdb
> ERROR: Comparing atoms
> .R<DMP 1>.A<C1N 115>,
> .R<DMP 1>.A<H41 2>,
> .R<DMP 1>.A<H42 3>, and
> .R<DMP 1>.A<H43 4>
> to atoms
> .R<DMP 1>.A<C2M 5>,
> .R<DMP 1>.A<C1N 115>,
> .R<DMP 1>.A<H43 4>, and
> .R<DMP 1>.A<H41 2>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 140
> !FATAL: Message: Atom named C2M from DMP did not match !
> !

I think we will need to see the entire list of LEaP commands you used (try
to make a test case that is as simple as possible.) In particular, we need
to see whatever file you have that defines the DMP residue (prepin, mol2,
etc.). The say in which "connection" atoms are defined is probably key
to this problem. Also, please indicate how you constructed this DMP file.


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