Thank you for your reply, Tsjerk!<br><br>I used gmxcheck, and got exactly the same number of atoms in xtc file as #proteinAtoms+#calciumAtoms+#chlorideAtom.<br><br>I also checked my mdp file. It does have "xtc_grps = protein Ca Cl". <br>
<br>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:<br>Protein_A 1<br>Na 15<br>Cl 12<br>
SOL 7254<br>And, in mdp file, I had: xtc_grps = protein Ca Na Cl<br><br>But this time, I didn't add any Na+ ion. After genion step, the end of the .top file became:<br>Protein_A 1<br>SOL 7280<br>Na 0<br>
Cl 1<br>In mdp file, I had: xtc_grps = protein Ca Cl<br><br>Will this difference cause the problem? How should I solve it? Thanks a lot!<br><br>Peggy<br><br><div class="gmail_quote">On Thu, Apr 10, 2008 at 12:22 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Peggy,<br>
<br>
I suspect that in your .mdp file you have a line<br>
<br>
xtc-grps = Protein<br>
<br>
This means that the xtc file will only contain those atoms which<br>
gromacs reckognizes as amino acids, based on the list in the file<br>
aminoacids.dat. Your .tpr file which is used to base the index on,<br>
contains all atoms, including the Ca/Cl. You can easily check how many<br>
atoms there are in your xtc file using gmxcheck and compare this to<br>
the groups you see based on the .tpr as you've given. If you need the<br>
calcium and chloride in the trajectory while you've only written<br>
Protein, you'll have to redo the simulation, changing the xtc-grps<br>
line in the .mdp, copy the file aminoacids.dat and add the ions to it<br>
or use an index file when running grompp. Of course you can first have<br>
a look at teh .trr file which contains all atoms by definition, but<br>
that is usually written much less frequent.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="Wj3C7c"><br>
On Thu, Apr 10, 2008 at 8:27 AM, Peggy Yao <<a href="mailto:peggy.yao@gmail.com">peggy.yao@gmail.com</a>> wrote:<br>
> Hi all,<br>
><br>
> In my system, I have 1 protein, 2 calcium atoms, and 1 chloride atom. When I<br>
> used trjconv to write the protein out as PDB file, it worked fine. However,<br>
> when I tried to write the calciums and chloride out using the same command<br>
> (but selecting different group to write out), I got the following fatal<br>
> error:<br>
><br>
> for calcium:<br>
> Select group for output<br>
> Opening library file /usr/share/gromacs/top/aminoacids.dat<br>
> Group 0 ( System) has 22737 elements<br>
> Group 1 ( Protein) has 894 elements<br>
> Group 2 ( Protein-H) has 707 elements<br>
> Group 3 ( C-alpha) has 89 elements<br>
> Group 4 ( Backbone) has 267 elements<br>
> Group 5 ( MainChain) has 357 elements<br>
> Group 6 (MainChain+Cb) has 440 elements<br>
> Group 7 ( MainChain+H) has 447 elements<br>
> Group 8 ( SideChain) has 447 elements<br>
> Group 9 ( SideChain-H) has 350 elements<br>
> Group 10 ( Prot-Masses) has 894 elements<br>
> Group 11 ( Non-Protein) has 21843 elements<br>
> Group 12 ( Ca) has 2 elements<br>
> Group 13 ( SOL) has 21840 elements<br>
> Group 14 ( Cl) has 1 elements<br>
> Group 15 ( Other) has 21843 elements<br>
> Select a group: 12<br>
> Selected 12: 'Ca'<br>
> Reading frame 0 time 0.000<br>
> Precision of traj.xtc is 0.001 (nm)<br>
> Segmentation fault 3 time 150.000 -> frame 3 time 150.000<br>
><br>
> for chloride:<br>
> Select group for output<br>
> Opening library file /usr/share/gromacs/top/aminoacids.dat<br>
> Group 0 ( System) has 22737 elements<br>
> Group 1 ( Protein) has 894 elements<br>
> Group 2 ( Protein-H) has 707 elements<br>
> Group 3 ( C-alpha) has 89 elements<br>
> Group 4 ( Backbone) has 267 elements<br>
> Group 5 ( MainChain) has 357 elements<br>
> Group 6 (MainChain+Cb) has 440 elements<br>
> Group 7 ( MainChain+H) has 447 elements<br>
> Group 8 ( SideChain) has 447 elements<br>
> Group 9 ( SideChain-H) has 350 elements<br>
> Group 10 ( Prot-Masses) has 894 elements<br>
> Group 11 ( Non-Protein) has 21843 elements<br>
> Group 12 ( Ca) has 2 elements<br>
> Group 13 ( SOL) has 21840 elements<br>
> Group 14 ( Cl) has 1 elements<br>
> Group 15 ( Other) has 21843 elements<br>
> Select a group: 14<br>
> Selected 14: 'Cl'<br>
> Reading frame 0 time 0.000<br>
> Precision of traj.xtc is 0.001 (nm)<br>
> -------------------------------------------------------<br>
> Program trjconv, VERSION 3.3.2<br>
> Source code file: gmx_trjconv.c, line: 994<br>
> Fatal error:<br>
> Index[0] 22737 is larger than the number of atoms in the trajectory file<br>
> (897)<br>
> -------------------------------------------------------<br>
><br>
> Does anybody know what might be wrong? Maybe the .tpr or .xtc files are not<br>
> complete? Is there any way to check? Thanks!<br>
><br>
> Peggy<br>
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><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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</blockquote></div><br>