Re: AMBER: unknown elements

From: David A. Case <>
Date: Wed, 15 Dec 2004 10:00:32 -0800

On Wed, Dec 15, 2004, Youyi Peng wrote:

> My proteins have three nonstandard residues. I made separate prep files for
> them. There is no problems for XLEAP with AMBER7 on Linux and Unix machines.
> However with AMBER8, XLEAP complains there are unknown elements on Linux
> machines. And I found out that the unknown elements come form the
> nonstandard residues. Anybody met this problem before? Any suggestions are
> welcome. Thanks a lot in advance.

It would be nice to see the actual messages from LEaP, but these are probably
innocuous warnings. You probably need to include addAtomTypes in your LEaP
script (see the leaprc.* files), in order to get the hybridizations correct.
But LEaP doesn't really need to know that information for other than graphical

It's hard to say more based on the information you provided, however.


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Received on Wed Dec 15 2004 - 18:53:00 PST
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