Kwee Hong wrote:
Alright..
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 guess.
So how can I generate the structure file I needed?
I've never tried it myself, but editconf purports to write CONECT records when
it extracts a structure from a .tpr file. You could construct a .tpr using the
desired frame, then try to convert it to a .pdb file with CONECT records. Other
than that, there may be some VMD tricks to get it to work, but I can't comment
there.
-Justin
Thanks.
Regards,
Joyce
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Gromacs Users' List <gmx-users@gromacs.org>
*Sent:* Wednesday, October 20, 2010 2:25:26
*Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms
with index 0.
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 <mailto:jalem...@vt.edu>>
> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto: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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--
========================================
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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