<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:14pt"><div><span class="Apple-style-span" style="font-family: arial, sans-serif; color: rgb(51, 51, 51); "><span class="hps"><span class="Apple-style-span" style="font-size: 18px; ">If I</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">do not</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">use for insert</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">ions</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size:
large;">into the water</span></span><span class="hps"><span class="Apple-style-span" style="font-size: large;"> from genion and </span></span></span><span class="Apple-style-span" style="font-family: arial, sans-serif; color: rgb(51, 51, 51); "><span class="hps"><span class="Apple-style-span" style="font-size: large;">Ions put</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">in the</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">file</span></span></span><span class="Apple-style-span" style="font-family: arial, sans-serif; color: rgb(51, 51, 51); "><span class="Apple-style-span" style="font-size: large;"> pdb w</span></span><span class="Apple-style-span" style="font-family: arial, sans-serif; color: rgb(51, 51, 51); "><span
class="Apple-style-span" style="font-size: large;">hether Gromacs n</span></span><span class="Apple-style-span" style="font-family: arial, sans-serif; color: rgb(51, 51, 51); "><span class="hps"><span class="Apple-style-span" style="font-size: large;">o problem</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: 18px; ">with it ?</span></span></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; color: rgb(51, 51, 51); "><span class="hps"><span class="Apple-style-span" style="font-size: large;"><br></span></span></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 24px; color: rgb(51, 51, 51); "><span class="hps"><span class="Apple-style-span" style="font-size: large;">Whether t</span><span class="hps"><span class="Apple-style-span" style="font-size:
large;">he</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">behavior</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">of ions</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">such as</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">ions</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: large;">that</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span"
style="font-size: large;">enter</span></span><span class="Apple-style-span" style="font-size: large;"> </span><span class="hps"><span class="Apple-style-span" style="font-size: 18px; ">via genion ?</span></span><br></span></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 24px; color: rgb(51, 51, 51); "><span class="hps"><span class="hps"><span class="Apple-style-span" style="font-size: 18px; "><br></span></span></span></span></div><div><font class="Apple-style-span" color="#333333" face="arial, sans-serif" size="5"><span class="Apple-style-span" style="font-size: 18px;">4.pdb :</span></font></div><div><font class="Apple-style-span" color="#333333" face="arial, sans-serif" size="5"><span class="Apple-style-span" style="font-size: 18px;"><br></span></font></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 24px; color: rgb(51, 51, 51); "><span class="hps"><span
class="hps"><span class="Apple-style-span" style="font-size: 18px; "><div>ATOM 1 CL CL 145 23.580 24.000 -0.020 1.00 0.00 </div><div>ATOM 2 CL CL 343 10.530 15.620 16.980 1.00 0.00 </div><div>ATOM 3 CL CL 344 16.530 6.620 25.980 1.00 0.00 </div><div>ATOM 4 CL CL 345 16.530 20.620 35.980 1.00 0.00 </div><div>ATOM 5 CL CL 346 22.530 10.620 13.980 1.00 0.00
</div><div>ATOM 6 CL CL 347 22.530 20.620 28.980 1.00 0.00 </div><div>ATOM 7 CL CL 348 20.530 8.020 9.980 1.00 0.00 </div><div>ATOM 8 Na Na 349 20.530 30.620 31.980 1.00 0.00 </div><div>ATOM 9 Na Na 350 20.530 4.620 29.980 1.00 0.00 </div><div>ATOM 10 Na Na 351 15.530 40.620 7.980 1.00 0.00 </div><div>ATOM 11
Na Na 352 15.530 10.620 19.980 1.00 0.00 </div><div>ATOM 12 Na Na 353 30.530 16.620 24.980 1.00 0.00 </div><div>ATOM 13 Na Na 354 40.530 15.620 19.980 1.00 0.00 </div><div>ATOM 14 Na Na 355 10.530 22.620 34.980 1.00 0.00 </div><div><br></div><div>topol.top :</div><div><br></div><div><div>;</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>File 'topol.top' was generated</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>By user: onbekend (0)</div><div>;<span class="Apple-tab-span"
style="white-space:pre">        </span>On host: onbekend</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>At date: Wed Nov 2 10:28:56 2011</div><div>;</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>This is a standalone topology file</div><div>;</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>It was generated using program:</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>pdb2gmx - VERSION 4.5.5</div><div>;</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>Command line was:</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>pdb2gmx -f 4.pdb -posrefc 0 </div><div>;</div><div>;<span class="Apple-tab-span" style="white-space:pre">        </span>Force field was read from the standard Gromacs share directory.</div><div>;</div><div><br></div><div>; Include forcefield parameters</div><div>#include
"gromos53a6.ff/forcefield.itp"</div><div><br></div><div>[ moleculetype ]</div><div>; Name nrexcl</div><div>Ion 1</div><div><br></div><div>[ atoms ]</div><div>; nr type resnr residue atom cgnr charge mass typeB chargeB massB</div><div>; residue 145 CL rtp CL q -1.0</div><div> 1 CL- 145 CL CL 1 -1 35.453 ; qtot -1</div><div>; residue 343 CL rtp CL q -1.0</div><div> 2 CL- 343 CL CL 2 -1 35.453 ; qtot
-2</div><div>; residue 344 CL rtp CL q -1.0</div><div> 3 CL- 344 CL CL 3 -1 35.453 ; qtot -3</div><div>; residue 345 CL rtp CL q -1.0</div><div> 4 CL- 345 CL CL 4 -1 35.453 ; qtot -4</div><div>; residue 346 CL rtp CL q -1.0</div><div> 5 CL- 346 CL CL 5 -1 35.453 ; qtot -5</div><div>; residue 347 CL rtp CL q -1.0</div><div> 6 CL- 347 CL CL
6 -1 35.453 ; qtot -6</div><div>; residue 348 CL rtp CL q -1.0</div><div> 7 CL- 348 CL CL 7 -1 35.453 ; qtot -7</div><div>; residue 349 Na rtp NA q +1.0</div><div> 8 NA+ 349 Na Na 8 1 22.9898 ; qtot -6</div><div>; residue 350 Na rtp NA q +1.0</div><div> 9 NA+ 350 Na Na 9 1 22.9898 ; qtot -5</div><div>; residue 351 Na rtp NA q +1.0</div><div> 10
NA+ 351 Na Na 10 1 22.9898 ; qtot -4</div><div>; residue 352 Na rtp NA q +1.0</div><div> 11 NA+ 352 Na Na 11 1 22.9898 ; qtot -3</div><div>; residue 353 Na rtp NA q +1.0</div><div> 12 NA+ 353 Na Na 12 1 22.9898 ; qtot -2</div><div>; residue 354 Na rtp NA q +1.0</div><div> 13 NA+ 354 Na Na 13 1 22.9898 ; qtot -1</div><div>; residue 355 Na
rtp NA q +1.0</div><div> 14 NA+ 355 Na Na 14 1 22.9898 ; qtot 0</div><div><br></div><div>; Include Position restraint file</div><div>#ifdef POSRES</div><div>#include "posre.itp"</div><div>#endif</div><div><br></div><div>; Include water topology</div><div>#include "gromos53a6.ff/spce.itp"</div><div><br></div><div>#ifdef POSRES_WATER</div><div>; Position restraint for each water oxygen</div><div>[ position_restraints ]</div><div>; i funct fcx fcy fcz</div><div> 1 1 1000 1000 1000</div><div>#endif</div><div><br></div><div>; Include topology for ions</div><div>#include "gromos53a6.ff/ions.itp"</div><div><br></div><div>[ system
]</div><div>; Name</div><div>Protein in water</div><div><br></div><div>[ molecules ]</div><div>; Compound #mols</div><div>Ion 1</div><div><br></div></div><div><br></div></span></span></span></span></div></div></body></html>