<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi Justin</div><div><br></div><div>The difference in my <br><span></span></div><div><br></div><div> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'</div><div><br></div><div>and your</div><div><br></div><div>g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of resname ISO'</div><div><br></div><div>is, that the last ISO is not in quotation marks. Could you please explain? <br></div><div><br></div><div>With your command I got this time no error but I got other stuff that I don't understand: <br></div><div><br></div><div>1.)</div><div> I got this warnings:</div><div><br></div><div>WARNING: masses and atomic (Van der Waals) radii will be determined<br> based on residue and atom names. These
numbers can deviate<br> from the correct mass and radius of the atom type.<br><br><br>WARNING: if there are broken molecules in the trajectory file,<br> they can not be made whole without a run input file<br></div><div><br></div><div>Can I ignore this or is this serious? <br></div><div><br></div><div>2.)</div><div>My output is one file called size.xvg. It contains</div><div><br></div><div># This file was created Sat Apr 14 16:55:56 2012<br># by the following command:<br># g_select -s molecule_in_water.pdb -select "Close to ISO" resname SOL and within 0.5 of resname ISO<br>#<br># g_select is part of G R O M A C S:<br>#<br># Green Red Orange Magenta Azure Cyan Skyblue<br>#<br>@ title "Selection size"<br>@ xaxis label "Time (ps)"<br>@ yaxis label "Number"<br>@TYPE xy<br>#
Selections:<br># "Close to ISO" resname SOL and within 0.5 of resname ISO<br>#<br>@ view 0.15, 0.15, 0.75, 0.85<br>@ legend on<br>@ legend box on<br>@ legend loctype view<br>@ legend 0.78, 0.8<br>@ legend length 2<br>@ s0 legend "Close to ISO"<br> 0.000 848.000<br><br></div><div>What is the interpretation of this? What I need is a new pdb. file that has to contain only the molecule ISO and the water layer SOL around it. Is this possible with g_select?</div><div><br></div><div>Thanks for helping me. <br></div><div>Greetings</div><div>Lara<br></div><div><br></div><div><br></div><div>p.s.</div><div>I use yahoo. I tried to find an "answer to all" option or something like that. Again after pressing answer the mail should go only to Justin. I put the mailing list in cc. Is here someone using yahoo also and know how to fix
this?<br></div><div><br></div><div><br><span></span></div><div><br><span></span></div><div><span></span></div><div><br></div> <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"> <hr size="1"> <b><span style="font-weight:bold;">Von:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">An:</span></b> Lara Bunte <lara.bunte@yahoo.de>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Gesendet:</span></b> 16:56 Samstag, 14.April 2012<br> <b><span style="font-weight: bold;">Betreff:</span></b> Re: [gmx-users] File editing - only one layer of water around a molecule<br> </font> </div> <br><br><br>Lara Bunte wrote:<br>> I still got the problem. What is wrong in this command:<br>> <br>>
g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'<br>> <br>> In the pdb. file ISO is for the molecule and SOL for the water.<br>> <br>> Please help<br>> <br><br>The above command assumes "ISO" is a default group, like "Protein" or something else. You can make selections based on any arbitrary residue name with something like the following:<br><br>g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of resname ISO'<br><br>Does that work?<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br> </div> </div> </div></body></html>