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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > 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@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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