[gmx-users] Bad .tpr or .xtc files?
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Apr 11 09:25:25 CEST 2008
Hi Peggy,
This is very much basic stuff for which you should refer to the
manual/wiki. E.g. on the index file, look at
http://wiki.gromacs.org/index.php/Index_File
For the other questions, check the manpages of editconf, trjconv and tpbconv.
Cheers,
Tsjerk
On Thu, Apr 10, 2008 at 11:03 PM, Peggy Yao <peggy.yao at gmail.com> wrote:
> Thank you for the explanation!
>
> In fact, 2 Ca atoms are a part of the protein. They are in the PDB file
> passed to pdb2gmx. Water molecules are added after the protein atoms and the
> Ca atoms, as in the PDB file after genbox. So I suppose, in the .tpr file,
> atoms should be ordered as protein-Ca-water-Cl?
>
> If I still have to do what you suggested, could you kindly tell me:
> 1. what is an index file?
> 2. how to make an index file to extract the matching set of atoms from .tpr
> file?
> 3. how to write a matching reference structure?
>
> Thanks a lot!
>
> Peggy
>
>
>
> On Thu, Apr 10, 2008 at 11:52 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
> > Hi Peggy,
> >
> > The key thing is that there's a mismatch between your .tpr file and
> > your .xtc file. The first is used for the indexing and it may very
> > well be that there's stuff in between the protein and the calcium.
> > That way, the index number for Ca, which should be N(protein) + 1, is
> > actually N(protein) + N(solvent) + 1. Now the list of atoms in the
> > .xtc file is only N(protein) + N(Ca) + N(Cl) and the atom you're
> > trying to fetch brings you to a part of memory you're not allowed to
> > touch (index > N(protein) + N(Ca) + N(Cl)): a segmentation fault
> >
> > But since you did write out correctly, the solution is simple. First
> > make an index file to extract the matching set of atoms from the .tpr
> > file. Then write a matching reference structure. If you really need a
> > matching .tpr file, you can do it with tpbconv. Now with a matching
> > reference structure, you can do just what you want...
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> >
> >
> > On Thu, Apr 10, 2008 at 6:42 PM, Peggy Yao <peggy.yao at gmail.com> wrote:
> > > Thank you for your reply, Tsjerk!
> > >
> > > I used gmxcheck, and got exactly the same number of atoms in xtc file as
> > > #proteinAtoms+#calciumAtoms+#chlorideAtom.
> > >
> > > I also checked my mdp file. It does have "xtc_grps = protein Ca Cl".
> > >
> > > In previous similar runs, I successfully wrote these atoms out. The only
> > > difference is that, in previous runs, I added some Na+ ions too. At the
> end
> > > of the .top file, I had:
> > > Protein_A 1
> > > Na 15
> > > Cl 12
> > > SOL 7254
> > > And, in mdp file, I had: xtc_grps = protein Ca Na Cl
> > >
> > > But this time, I didn't add any Na+ ion. After genion step, the end of
> the
> > > .top file became:
> > > Protein_A 1
> > > SOL 7280
> > > Na 0
> > > Cl 1
> > > In mdp file, I had: xtc_grps = protein Ca Cl
> > >
> > > Will this difference cause the problem? How should I solve it? Thanks a
> lot!
> > >
> > > Peggy
> > >
> > >
> > >
> > > On Thu, Apr 10, 2008 at 12:22 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > > wrote:
> > >
> > > > Hi Peggy,
> > > >
> > > > I suspect that in your .mdp file you have a line
> > > >
> > > > xtc-grps = Protein
> > > >
> > > > This means that the xtc file will only contain those atoms which
> > > > gromacs reckognizes as amino acids, based on the list in the file
> > > > aminoacids.dat. Your .tpr file which is used to base the index on,
> > > > contains all atoms, including the Ca/Cl. You can easily check how many
> > > > atoms there are in your xtc file using gmxcheck and compare this to
> > > > the groups you see based on the .tpr as you've given. If you need the
> > > > calcium and chloride in the trajectory while you've only written
> > > > Protein, you'll have to redo the simulation, changing the xtc-grps
> > > > line in the .mdp, copy the file aminoacids.dat and add the ions to it
> > > > or use an index file when running grompp. Of course you can first have
> > > > a look at teh .trr file which contains all atoms by definition, but
> > > > that is usually written much less frequent.
> > > >
> > > > Cheers,
> > > >
> > > > Tsjerk
> > > >
> > > >
> > > >
> > > >
> > > > On Thu, Apr 10, 2008 at 8:27 AM, Peggy Yao <peggy.yao at gmail.com>
> wrote:
> > > > > Hi all,
> > > > >
> > > > > In my system, I have 1 protein, 2 calcium atoms, and 1 chloride
> atom.
> > > When I
> > > > > used trjconv to write the protein out as PDB file, it worked fine.
> > > However,
> > > > > when I tried to write the calciums and chloride out using the same
> > > command
> > > > > (but selecting different group to write out), I got the following
> fatal
> > > > > error:
> > > > >
> > > > > for calcium:
> > > > > Select group for output
> > > > > Opening library file /usr/share/gromacs/top/aminoacids.dat
> > > > > Group 0 ( System) has 22737 elements
> > > > > Group 1 ( Protein) has 894 elements
> > > > > Group 2 ( Protein-H) has 707 elements
> > > > > Group 3 ( C-alpha) has 89 elements
> > > > > Group 4 ( Backbone) has 267 elements
> > > > > Group 5 ( MainChain) has 357 elements
> > > > > Group 6 (MainChain+Cb) has 440 elements
> > > > > Group 7 ( MainChain+H) has 447 elements
> > > > > Group 8 ( SideChain) has 447 elements
> > > > > Group 9 ( SideChain-H) has 350 elements
> > > > > Group 10 ( Prot-Masses) has 894 elements
> > > > > Group 11 ( Non-Protein) has 21843 elements
> > > > > Group 12 ( Ca) has 2 elements
> > > > > Group 13 ( SOL) has 21840 elements
> > > > > Group 14 ( Cl) has 1 elements
> > > > > Group 15 ( Other) has 21843 elements
> > > > > Select a group: 12
> > > > > Selected 12: 'Ca'
> > > > > Reading frame 0 time 0.000
> > > > > Precision of traj.xtc is 0.001 (nm)
> > > > > Segmentation fault 3 time 150.000 -> frame 3 time
> 150.000
> > > > >
> > > > > for chloride:
> > > > > Select group for output
> > > > > Opening library file /usr/share/gromacs/top/aminoacids.dat
> > > > > Group 0 ( System) has 22737 elements
> > > > > Group 1 ( Protein) has 894 elements
> > > > > Group 2 ( Protein-H) has 707 elements
> > > > > Group 3 ( C-alpha) has 89 elements
> > > > > Group 4 ( Backbone) has 267 elements
> > > > > Group 5 ( MainChain) has 357 elements
> > > > > Group 6 (MainChain+Cb) has 440 elements
> > > > > Group 7 ( MainChain+H) has 447 elements
> > > > > Group 8 ( SideChain) has 447 elements
> > > > > Group 9 ( SideChain-H) has 350 elements
> > > > > Group 10 ( Prot-Masses) has 894 elements
> > > > > Group 11 ( Non-Protein) has 21843 elements
> > > > > Group 12 ( Ca) has 2 elements
> > > > > Group 13 ( SOL) has 21840 elements
> > > > > Group 14 ( Cl) has 1 elements
> > > > > Group 15 ( Other) has 21843 elements
> > > > > Select a group: 14
> > > > > Selected 14: 'Cl'
> > > > > Reading frame 0 time 0.000
> > > > > Precision of traj.xtc is 0.001 (nm)
> > > > > -------------------------------------------------------
> > > > > Program trjconv, VERSION 3.3.2
> > > > > Source code file: gmx_trjconv.c, line: 994
> > > > > Fatal error:
> > > > > Index[0] 22737 is larger than the number of atoms in the trajectory
> file
> > > > > (897)
> > > > > -------------------------------------------------------
> > > > >
> > > > > Does anybody know what might be wrong? Maybe the .tpr or .xtc files
> are
> > > not
> > > > > complete? Is there any way to check? Thanks!
> > > > >
> > > > > Peggy
> > > > > _______________________________________________
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Tsjerk A. Wassenaar, Ph.D.
> > > > Junior UD (post-doc)
> > > > Biomolecular NMR, Bijvoet Center
> > > > Utrecht University
> > > > Padualaan 8
> > > > 3584 CH Utrecht
> > > > The Netherlands
> > > > P: +31-30-2539931
> > > > F: +31-30-2537623
> > > > _______________________________________________
> > > > gmx-users mailing list gmx-users at gromacs.org
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> > > >
> > >
> > >
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> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> >
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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