Re: Vanishing bonds in small molecule during psf generation.

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jul 18 2007 - 11:29:36 CDT

I don't see an O1' C1' bond defined in the topology file. Also,
your PA O5* bond is written "PA 05*" (i.e. your letter O is actually
a zero).

Additionally, you should use "first none last none" in your segment
definition in psfgen so that you don't get default termini that just
get stuck at the origin.

If I had to guess, the reason manually adding the bonds didn't work
is because you also have to change the NBOND number in the psf.

On Jul 18, 2007, at 8:58 AM, Christian Blouin wrote:

> Greetings,
>
>
>
> 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 :http://morticia.cs.dal.ca/
> files/GlcNAc.zip . 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!
>
>
>
> Regards,
>
>
>
>
>
>
>
> --------------------------------------------------------------
>
> Christian Blouin, Asst. Prof.
>
> Biochemistry AND Computer Science
>
> Dalhousie University
>
> http://morticia.cs.dal.ca/lab_public
>
>
>
>

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