<div>Hi all,</div>
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<div>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:</div>
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<div>for calcium:</div>
<div>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</div>
<div> </div>
<div>for chloride:</div>
<div>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)</div>
<div>-------------------------------------------------------<br>Program trjconv, VERSION 3.3.2<br>Source code file: gmx_trjconv.c, line: 994</div>
<div>Fatal error:<br>Index[0] 22737 is larger than the number of atoms in the trajectory file (897)<br>-------------------------------------------------------<br></div>
<div>Does anybody know what might be wrong? Maybe the .tpr or .xtc files are not complete? Is there any way to check? Thanks!</div>
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<div>Peggy</div>