<div><font style="BACKGROUND-COLOR: #ffffff"></font> </div>
<div> </div>
<div>Hi </div>
<div>My simulation broke down and the simulation procedues are as follows.</div>
<div> </div>
<div>1. center a protein molecule in the simulation box</div>
<div>2. put 20 ligands around the protein with " genbox " command</div>
<div>3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software.</div>
<div>4. solvent addition , with the command " genbox <strong><font face="Courier New">-vdwd</font></strong> 0.2 " </div>
<div>5. Addition of ions, with the command " <span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">genion "</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">6. Energy minimization of the solvated system</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">7. Position restrained MD</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=> simulation broke down.</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=> It is very probable that some molecule clashing with another.</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=> since i have made sured that any atom of the ligands does not overlap on any atom of the protein with Visulization-software, </span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"> the clashed pair of the molecules are possible " solvent vs solvent " or "solvent vs protein" or "solvent vs ligand " </span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=> however, from the Gromacs manual , command "genbox"</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"> " Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less </span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"> than the sum of the VanderWaals radii of both atoms. A database (<tt>vdwradii.<a href="http://manual.gromacs.org/current/online/dat.html">dat</a></tt>) of VanderWaals radii is read by the program, atoms not in the </span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"> database are assigned a default distance <tt>-vdw</tt>."</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=> here is </span><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">vdwradii.dat (the ligand is simply made of C, N, O, H)<br>
; Very approximate VanderWaals radii<br>; only used for drawing atoms as balls or for calculating atomic overlap.<br>; longest matches are used<br>; '???' or '*' matches any residue name<br>; 'AAA' matches any protein residue name<br>
??? C 0.15<br>??? F 0.12<br>??? H 0.04<br>??? N 0.110<br>??? O 0.105<br>??? S 0.16<br></span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">My questions are </span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">1. anything wrong of my simulation procedures ?</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">2. how to find the clashed molecules ? </span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">Thank you</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">Lin</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"> </span></div>