Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages

From: David A Case <>
Date: Mon, 30 Dec 2013 07:41:41 -0500

On Mon, Dec 30, 2013, Yip Yew Mun wrote:
> Thanks for the prompt reply. However, the PDB which I loaded into tleap
> already had the connect records removed. Is it possible these records
> remain hidden after removal? Nonetheless, when I desc those atoms, tleap
> states that there is a single bond present.

LEaP automatically adds amide bonds between adjacent peptide groups (because
this is requested in the amino library files themselves.)

It is *possible* to change this behavior, but that requires a lot of knowledge
of how Amber does things, and seems pointless if you are going to add these
bonds back anyway. Maybe you should give some context to what you are really
trying to accomplish here.


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Received on Mon Dec 30 2013 - 05:00:02 PST
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