Re: how add bond in psf file?

From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Mon Sep 25 2006 - 11:09:11 CDT

Hi Jerome,
Thank you.
I use a not standard topology. I created my psf-file with psfgen than I
modified it.
I want fix distance atoms like this:
A_Molecule-O---H---O-Molecule_B where O--H and H--O are 1.5 Ang.
I do not want fix atoms but only two distance with stretching coordinate.
At this moment I see that there is a "sanity check" in hydrogen bond in
routine Molecule_*.C of namd source.
This not permit extra bond for only hydrogen atom...

Thanks
Luca

> Most likely, there is a way to generate this PSF file with the extra bond,
> and it will have a higher chance of being consistent. Was the file created
> using psfgen? Or CHARMM? Are you using a custom topology? In most cases,
> you should be able to either add the bond directly to the residue topology,
> or use a patch.
>
> Jerome
>
> On Monday 25 September 2006 09:18, Luca Bellucci wrote:
> > Hi all,
> > How add bond in psf_file?
> > When I try to add bond in psf_file I obtain
> > this ERROR:
> >
> > FATAL ERROR: Atom 1300 has bad group size. Check for duplicate bonds.
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: Atom 1300 has bad group size. Check for duplicate
> > bonds.
> >
> > Thanks
> > Luca

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