VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 19 2010 - 22:04:44 CDT

On Tue, Oct 19, 2010 at 10:58 PM, Joyce Tan <joyce.tankh_at_gmail.com> wrote:
> FYI.
>
> I've post a message to gromacs mailing list and Justin A. Lemkul pointed out
> that my topology does not correspond to a MARTINI coarse-grained topology.
> As such, probably a bunch of the pattern matching is getting incorrect
> information.  So, I cannot use top2psf.pl with this type of topology which
> was created for a very specific purpose and requires that format.

i guess john and i confused the script with this one.

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/

the download says top2psf.tcl, but it is a perl script.

cheers,
    axel.

> Anyway, thanks for you help.
>
> Cheers,
> Joyce
>
> On Wed, Oct 20, 2010 at 1:53 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> 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.
>
> 

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