Re: AMBER: Connecting two ethanes in LEaP

From: David A. Case <>
Date: Fri, 31 Aug 2007 09:18:18 -0700

On Thu, Aug 30, 2007, Kliman, Michal wrote:

> 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 don't think that I would understand what you really want to do when you
say "join two ethane molecules", and I am sure that LEaP doesn't know either.
An ethane molecule doesn't have "head" and "tail" atoms designed to become
part of a polymer. You either have to do this by hand (say in xleap) or
remove some hydrogens (I assume) from the ethane fragments and designate
"conect1" and "conect2" atoms. Take a look at how the sequence command works
for amino acid fragments, and try to do something along the same lines.


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Received on Sun Sep 02 2007 - 06:07:34 PDT
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