VMD-L Mailing List

From: Joyce Tan (joyce.tankh_at_gmail.com)
Date: Tue Oct 19 2010 - 21:58:16 CDT

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.

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/ <http://www.ks.uiuc.edu/%7Ejohns/> 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.
>