Re: how add bond in psf file?

From: Jim Phillips (
Date: Mon Sep 25 2006 - 14:05:27 CDT

NAMD takes bonds seriously, since they are used to derive exclusions.

Your best option is to implement that H-O restraint in TclForces.


On Mon, 25 Sep 2006, Luca Bellucci wrote:

> 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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