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