AMBER Archive (2007)

Subject: Re: AMBER: Connecting two ethanes in LEaP

From: David A. Case (case_at_scripps.edu)
Date: Fri Aug 31 2007 - 11:18:18 CDT

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.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu