<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div>Dear Gromacs users</div><div>I want to calculate SDF for water molecules around protein.</div><div><br></div><div>I use these command line:</div><div><span style="color: rgb(0, 0, 191);">trjconv -s ../md_0_1.tpr -f ../md_0_1.xtc -o first.xtc -boxcenter tric -ur compact -pbc none</span><br><span style="color: rgb(0, 0, 0);">This asks me to </span></div><div><span style="color: rgb(0, 96, 191);">Select <span style="color: rgb(191, 0, 95);">group for output</span></span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 0 ( System) has 41559 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 1 ( Protein) has 2698
elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 2 ( Protein-H) has 1351 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 3 ( C-alpha) has 165 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 4 ( Backbone) has 495 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 5 ( MainChain) has 661 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 6 ( MainChain+Cb) has 821 elements</span><br style="color: rgb(0, 96,
191);"><span style="color: rgb(0, 96, 191);">Group 7 ( MainChain+H) has 823 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 8 ( SideChain) has 1875 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 9 ( SideChain-H) has 690 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 10 ( Prot-Masses) has 2698 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 11 ( non-Protein) has 38861 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 12
( Water) has 38859 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 13 ( SOL) has 38859 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 14 ( non-Water) has 2700 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 15 ( Ion) has 2 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96, 191);">Group 16 ( NA+) has 2 elements</span><br style="color: rgb(0, 96, 191);"><span style="color: rgb(0, 96,
191);">Group 17 ( Water_and_ions) has 38861 ele</span>ments<br></div><div><br></div><div><span style="color: rgb(0, 0, 0);">Here I select group (13)</span></div><div><br><span style="color: rgb(0, 0, 0);"></span></div><div><span style="color: rgb(0, 0, 0);">Then this command line:</span></div><div><span style="color: rgb(0, 0, 0);"></span> <span style="color: rgb(0, 0, 191);">trjconv -s ../md_0_1.tpr -f first.xtc -o second.xtc -fit rot+trans</span></div><div><span style="color: rgb(0, 0, 0);">It asks for two groups:</span></div><div><span style="color: rgb(0, 0, 0);"></span><br>Select group for <span style="color: rgb(255, 0, 127);">least squares fit</span><br>Group 0 ( System) has 41559 elements<br>Group 1 ( Protein) has 2698 elements<br>Group 2
( Protein-H) has 1351 elements<br>Group 3 ( C-alpha) has 165 elements<br>Group 4 ( Backbone) has 495 elements<br>Group 5 ( MainChain) has 661 elements<br>Group 6 ( MainChain+Cb) has 821 elements<br>Group 7 ( MainChain+H) has 823 elements<br>Group 8 ( SideChain) has 1875 elements<br>Group 9 ( SideChain-H) has 690 elements<br>Group 10 ( Prot-Masses) has 2698 elements<br>Group 11 ( non-Protein) has 38861
elements<br>Group 12 ( Water) has 38859 elements<br>Group 13 ( SOL) has 38859 elements<br>Group 14 ( non-Water) has 2700 elements<br>Group 15 ( Ion) has 2 elements<br>Group 16 ( NA+) has 2 elements<br>Group 17 ( Water_and_ions) has 38861 elements<br style="color: rgb(0, 0, 191);"><br></div><div>Here I choose group (4) protein backbone</div><div>------ and then<br></div><div>Selected 4: 'Backbone'<br><span style="color: rgb(255, 0, 127);">Select group for output</span><br>Group 0
( System) has 41559 elements<br>Group 1 ( Protein) has 2698 elements<br>Group 2 ( Protein-H) has 1351 elements<br>Group 3 ( C-alpha) has 165 elements<br>Group 4 ( Backbone) has 495 elements<br>Group 5 ( MainChain) has 661 elements<br>Group 6 ( MainChain+Cb) has 821 elements<br>Group 7 ( MainChain+H) has 823 elements<br>Group 8 ( SideChain) has 1875 elements<br>Group 9
( SideChain-H) has 690 elements<br>Group 10 ( Prot-Masses) has 2698 elements<br>Group 11 ( non-Protein) has 38861 elements<br>Group 12 ( Water) has 38859 elements<br>Group 13 ( SOL) has 38859 elements<br>Group 14 ( non-Water) has 2700 elements<br>Group 15 ( Ion) has 2 elements<br>Group 16 ( NA+) has 2 elements<br>Group 17 ( Water_and_ions) has 38861 elements<br>Select a group:<br><br></div><div>again I select 13
for SOL</div><div>======================================Below is the <span style="color: rgb(191, 0, 95);">error</span> which I get:::::::::::::::::::<br></div><div><br></div><div><span style="color: rgb(96, 0, 191);">Back Off! I just backed up second.xtc to ./#second.xtc.5#</span><br style="color: rgb(96, 0, 191);"><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">-------------------------------------------------------</span><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">Program trjconv, VERSION 4.5.5</span><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">Source code file: gmx_trjconv.c, line: 1166</span><br style="color: rgb(96, 0, 191);"><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">Fatal error:</span><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">Index[36161] 38860 is larger than the number of atoms in the</span><br
style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">trajectory file (38859). There is a mismatch in the contents</span><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">of your -f, -s and/or -n files.</span><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">For more information and tips for troubleshooting, please check the GROMACS</span><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">website at http://www.gromacs.org/Documentation/Errors</span><br style="color: rgb(96, 0, 191);"><span style="color: rgb(96, 0, 191);">-------------------------------------------------------</span><br><br></div><div>=================================================================<br></div><div>I have checked my .gro file from which md_0_1.tpr has created. It has 41559 atoms</div><div>also in topology file I have one protein with 2698 atoms, 12953 water molecules (==38859 atoms) and
2 ions which gives in total 41559 atoms.</div><div>=========================================</div><div style="color: rgb(96, 0, 191);">************I do not undestand the error.</div><div>**********<span style="color: rgb(128, 0, 0);">Also please let me know if I want to calculate water SDF around protein backbone, are my group selections fine???</span></div><div><br></div><div>Thanks for your time</div><div>Regards</div><div>D.M<br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>and then</div><div><br></div><div><br></div><div><br></div><div></div></div></body></html>