Vanishing bonds in small molecule during psf generation.

From: Christian Blouin (
Date: Wed Jul 18 2007 - 08:58:13 CDT



            We've been wrestling with the setup for a small molecule for a
while now. We have hand made a topology definition for the molecule and
added it to one of the top_all27*.inp file. In the psf, two bonds refuse to
be added to the molecule on either side of a bis-phosphate. The bonds are
defined in the topology file, they show up if the PDB file is loaded by
itself, but not if the pdb is added to the generated psf. Manually adding
the bond in the psf's !NBOND section doesn't do anything. Here is a link to
an archive for the top, pdb and psf file : . The offending bonds are
involving atom PA and O5* as well as O1' to C1', or respectively in the psf
nomenclature: 43 and 46, 35 and 42.


            I suspect that the problem is minor, but I feel like I've
exhausted each one of my "good ideas" to get this molecule to work!







Christian Blouin, Asst. Prof.

Biochemistry AND Computer Science

Dalhousie University


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