AMBER: Connecting two ethanes in LEaP

From: Kliman, Michal <>
Date: Thu, 30 Aug 2007 15:53:46 -0500 (CDT)

Dear Amber community,
I would like to know how to connect two carbon chains in LEaP. When I try
to connect two ethane molecules one named ETH (C10, C11) the other ETD
(C12, C13) into ETL I get the FATAL error below:

(I am ultimately trying to join a carbon tail to a lipid headgroup charge
parameterized using Gaussian). Thanks. Michal

> ETL = sequence {ETH ETD}
ERROR: Comparing atoms
        .R<ETH 1>.A<C11 5>,
        .R<ETD 1>.A<H121 2>,
        .R<ETD 1>.A<H122 3>, and
        .R<ETD 1>.A<H123 4>
       to atoms
        .R<ETD 1>.A<C13 5>,
        .R<ETH 1>.A<C11 5>,
        .R<ETD 1>.A<H123 4>, and
        .R<ETD 1>.A<H121 2>
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named C13 from ETD did not match

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Received on Sun Sep 02 2007 - 06:07:24 PDT
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