From: Jerome Henin (jhenin_at_vitae.cmm.upenn.edu)
Date: Mon Sep 25 2006 - 10:16:03 CDT
Luca,
If you'll take my advice: simply do not add bonds to a PSF file, unless you
really know what you are doing.
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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