[gmx-users] Bad .tpr or .xtc files?
Peggy Yao
peggy.yao at gmail.com
Fri Apr 11 20:08:54 CEST 2008
Thank you, Tsjerk. I will check them out.
But I am still confursed with what has gone wrong. As I said in my previous
eamil, 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 so, I don't know
why when writing out Ca or Cl atoms, I got segmentation fault and index out
of bound errors.
Peggy
On Fri, Apr 11, 2008 at 12:25 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:
> 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
> > > > > > _______________________________________________
> > > > > > gmx-users mailing list gmx-users at gromacs.org
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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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> > > >
> > > >
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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
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> >
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
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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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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