AMBER Archive (2004)

Subject: Re: AMBER: (no subject)

From: David A. Case (
Date: Tue Dec 07 2004 - 07:00:49 CST

On Tue, Dec 07, 2004, Andrew Box wrote:
> I wish to know if you need to place all double bonds (or psuedo double
> bonds) on molecules before saving then as prmtop and inpcrd files. This is
> cause when i open my prepin files in xleap, my molecule of interest (and
> DNA strands) have no double bonds, even though i added the before i saved
> the prepin file.

The prepin file format knows nothing about single or double bonds, nor does
the underlying force field. If you need to store this information (for
example, to make pictures in some other program), use the mol2 format.


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