[gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 19 20:14:34 CEST 2010

Kwee Hong wrote:
> Hi,
> I've got a top2psf.pl script from the web and used it to generate a psf 
> file. Yet it generated  some bonds to atoms with index 0 which should 
> not occur.  It causes VMD cannot load it and had a segmentation fault. 
> vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf
> ERROR) Error reading bond information.
> Segmentation fault
> I wonder am I getting the right top2psf.pl.  Or is there any place I can 
> get the latest stable version of that script?

There is only one version.  Zeros are only printed if something goes wrong, i.e. 
you have provided the wrong input or something else has failed.

Based solely on the information you've provided I cannot diagnose what has gone 


> Here, I attached the perl script I used.
> Thanks.
> Regards,
> Joyce


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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