VMD-L Mailing List

From: Joyce Tan (joyce.tankh_at_gmail.com)
Date: Tue Oct 19 2010 - 22:41:27 CDT

Hi Axel & John,

I got my psf generated successfully using the script from the link provided
by Axel.
But I execute it as a perl script rather than tcl.

Thanks guys.

Cheers,
Joyce

On Wed, Oct 20, 2010 at 11:04 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>