VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 19 2010 - 12:53:31 CDT

hi,

just a quick note. gromacs .top files are typically "incomplete".
it uses preprocessing to build a full top file before generating
the (binary) tpr file that contains all runtime information for an MD run.

thus for the top2psf script to have a chance to work, you first need
to intercept the preprocessed .top file when calling grompp
and use that with top2psf. there is still good chances that it
will not work (well). the top file format is very flexible and writing
a generic parser for it can be challenging.

cheers,
    axel.

On Tue, Oct 19, 2010 at 1:03 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
>  Most likely there's a bug in that script.  I didn't write it, I just
> did a google search for "gromacs make psf file" to find it.  If you send
> me the PSF file it created, I can have a look at it and see what is wrong
> with it.  The segmentation fault shouldn't occur even with a badly formatted
> PSF file, so if you can send me that file, it would be helpful.
>
> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
> On Wed, Oct 20, 2010 at 12:58:00AM +0800, Joyce Tan wrote:
>>    John.
>>
>>    Thanks for your quick reply.
>>
>>    I've generated the psf with the script u provided. But I've a problem at
>>    loading it into vmd.
>>
>>    vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf
>>    ERROR) Error reading bond information.
>>    Segmentation fault
>>
>>    Why this happens?
>>
>>    I'm currently using vmd 1.8.7 on Ubuntu 10.04 64 bit.
>>
>>    On Wed, Oct 20, 2010 at 12:39 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>>      I believe the Gromacs tools come with a "top2psf.pl" PERL script
>>      that you might want to try out:
>>       http://www.gromacs.org/@api/deki/files/90/=top2psf.pl
>>      Cheers,
>>       John Stone
>>       vmd_at_ks.uiuc.edu
>>
>>      On Wed, Oct 20, 2010 at 12:04:36AM +0800, Joyce Tan wrote:
>>      >    ok. Thanks for your reply.
>>      >
>>      >    Can u point me how can I build the psf?
>>      >
>>      >    Thanks
>>      >
>>      >    On Tue, Oct 19, 2010 at 11:45 PM, John Stone <johns_at_ks.uiuc.edu>
>>      wrote:
>>      >
>>      >      Hi,
>>      >       In abscence of a structure file that explicitly specifies bond
>>      >      information,
>>      >      VMD uses a distance-based bond determination heuristic.  If you
>>      are
>>      >      seeing
>>      >      a bond where there should not be one, or you are expecting to see
>>      one
>>      >      but
>>      >      there isn't one, then you should try to create a PSF file or
>>      another
>>      >      structure file type that explicitly specifies the bonds for your
>>      >      structure
>>      >      so that VMD doesn't have to guess.
>>      >
>>      >      Cheers,
>>      >       John Stone
>>      >       vmd_at_ks.uiuc.edu
>>      >
>>      >      On Tue, Oct 19, 2010 at 11:36:43PM +0800, Joyce Tan wrote:
>>      >      >    Hi.
>>      >      >
>>      >      >    I have my 5000 frames .xtc and .gro loaded into vmd.
>>      >      >
>>      >      >    And I was trying to convert one of the frames into pdb
>>      through
>>      >      this:
>>      >      >
>>      >      >    set A [atomselect top protein frame 4998]
>>      >      >    $A writepdb xx.pdb
>>      >      >
>>      >      >    When I load xx.pdb into the vmd, one atom from one residue
>>      is
>>      >      connected to
>>      >      >    another atom from another residue. This particular bonding
>>      was not
>>      >      found
>>      >      >    in the trajectory file. I really don't understand why is
>>      this
>>      >      happening.
>>      >      >    Can someone help?
>>      >      >     Thanks.
>>      >      >
>>      >      >    Regards,
>>      >      >    Joyce
>>      >      --
>>      >      NIH Resource for Macromolecular Modeling and Bioinformatics
>>      >      Beckman Institute for Advanced Science and Technology
>>      >      University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>      >      Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>>      >       WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>>
>>      --
>>      NIH Resource for Macromolecular Modeling and Bioinformatics
>>      Beckman Institute for Advanced Science and Technology
>>      University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>      Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>>       WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.