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 <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@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
========================================
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