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

[Kwee Hong]

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?

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>
> *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
> 
> ========================================
> -- gmx-users mailing list    gmx-users at gromacs.org 
><mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or 
>send it to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 

-- ========================================

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

========================================
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101019/1d61ff58/attachment.html>