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

[Justin A. Lemkul]

Kwee Hong wrote:
> I executed the script at the therminal by typing
> perl top2psf.pl -i topol.top -o zz.psf
> Here, I attached my input file.
> 

Your topology does not correspond to a MARTINI coarse-grained topology.  As 
such, probably a bunch of the pattern matching is getting incorrect information. 
  You cannot use top2psf.pl with this type of topology.  It was created for a 
very specific purpose and requires that format, nothing else.

-Justin

> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wednesday, October 20, 2010 2:14:34
> *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms 
> with index 0.
> 
> 
> 
> 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 wrong.
> 
> -Justin
> 
>  > Here, I attached the perl script I used.
>  >
>  > Thanks.
>  >
>  > Regards,
>  > Joyce
>  >
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================