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

[Justin A. Lemkul]

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 <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 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto: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
> 
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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

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