<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>I am very sorry for bothering the list members with my previous email. I figured this myself, I just need to "reset" from the command line.</span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;">Sincerely,</div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;"><br><span></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style:
normal;"><span>Vis<br></span></div><br><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div dir="ltr"><font face="Arial" size="2"> <b><span style="font-weight: bold;">To:</span></b> "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, September 20, 2012 12:25 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> solvation box transformed<br> </font> </div> <br><div id="yiv106137876"><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;"><div>Dear Users,</div><div><br></div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;">I have some difficulties with reference frames when solvating a
protein. The essence of my problem as follows.</div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;">Chimera solvates a box using _untransformed_ coordinates, but if I try to write out the inpcrd/prmtop,</div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;">it writes out the _transformed_ coordinates, thus the box planes become no longer parallel to xyz axes, which does not
allow<br></div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;">to transfer the inpcrd coordinates to another program (NAMD).</div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;"><br></div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;">Of course, I could try a workaround by creating the protein and re-saving it before solvation, and then solvating it while avoiding any mouse movement,or using ambertool cooman line, but maybe there is another solution, or perhaps an "untransformed" button could be implemented in the prmtop tool?</div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times,
serif;background-color:transparent;font-style:normal;"><br></div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;">Sincerely,</div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;"><br></div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;">Vis<br></div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;"><br></div><div style="color:rgb(0, 0, 0);font-size:16px;font-family:times new roman, new york, times, serif;background-color:transparent;font-style:normal;"></div></div></div></div><br><br> </div> </div> </div></body></html>