[gmx-users] top2psf.pl is generating some bonds to atoms with index 0.
jestan1985 at yahoo.com
Wed Oct 20 08:37:08 CEST 2010
I actually simulated my protein for 5ns. Then I loaded the trajectory file and
.gro file in vmd. Then, I extracted one of the frame and write it into pdb
format, When I open it with vmd, one of the atom from a residue is connected to
another atom in another residue. Things like this happens as VMD uses a
distance-based bond determination heuristic. Therefore, I would need a structure
file which specifies the bonds for my structure so that VMD doesn't have to
So how can I generate the structure file I needed?
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Wednesday, October 20, 2010 2:25:26
Subject: Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index
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.
> *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
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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