AMBER Archive (2006)

Subject: Re: AMBER: preparing ligand/rna structure for MD

From: David A. Case (
Date: Mon Aug 28 2006 - 19:11:34 CDT

On Mon, Aug 28, 2006, wrote:
> I am doing some intercalation studies with various nucleic acid structures
> and small molecules. I created an intercalation site and used the software
> Chimera to dock a molecule of proflavine into the site by hand. What would
> I need to do before this structure would be ready for MD? Currently I can
> not open the file in xleap because I get a fatal bond atom error causing
> leap to crash.

Please post the file that causes leap to crash....this is not supposed to
happen. Also, seeing the exact error message would help (in case we don't see
the same problem you do.)


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