<div>I know what is happening... I am tired :)</div>
<div>I used previous pdb file before moving my complex and just realised after fighting so long, sorry for my message.</div>
<div> </div>
<div>Have a good weekend,</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Fri, Feb 10, 2012 at 2:54 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>Dear Gmx Users,</div>
<div> </div>
<div>I am preparing my protein-ligand complex system for Umbrella Sampling (free binding energy of ligand) and I set</div>
<div> up the box (Pulling with Z coordinate):</div>
<div> </div>
<div>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font size="3"><font face="Times New Roman">editconf -f Protein10LIGrot.pdb -o ProteinLIGbox.pdb -box 12 7 13</font></font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font size="3"><font face="Times New Roman"></font></font></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font size="3"><font color="#000000" face="Times New Roman">Then using VMD I placed my Protein-Lig complex to on the right side, saved coordinates of the system</font></font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font size="3"><font color="#000000" face="Times New Roman"> and tried to add water:</font></font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><span style="COLOR:red" lang="PL"></span></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><span style="COLOR:red" lang="PL">genbox -cp ProteinLIGbox.pdb -cs spc216.gro -o Solv.gro -p topol.top</span></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><span style="COLOR:red" lang="PL"></span></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><span style="COLOR:red" lang="PL"><font color="#000000">The problem is that after adding water gromacs move my Protein-Lig complex in the center of the the Z coordinate - center my complex... Why? I want it as it was just before adding water. Do you have any clue what is happening?</font></span></span></p>
<span class="HOEnZb"><font color="#888888">
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><span style="COLOR:red" lang="PL"><font color="#000000"></font></span></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><span style="COLOR:red" lang="PL"><font color="#000000">Steven</font></span></span></p></font></span></div></blockquote></div><br>