<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>Okay, after <br></div><div><br></div><div>g_select -f mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'<br></div><div><br></div><div>I got:</div><div><br></div><div>selection parser: invalid selection '"Close to ISO" resname SOL and within 0.5 of group "ISO"'</div><div><br>Input error or input inconsistency:<br>selection(s) could not be parsed<br><br></div><div>I also tried other permutations of ISO and SOL and got the same. <br></div><div><br></div><div>I read the complete help to g_select twice and I understand nothing what there is written. In general I like Gromacs more and more but g_select program is totally fucked. I don't get it. :-(</div><div><br></div><div>Greetings</div><div>Lara</div><div><br></div><div>p.s.</div><div>Here in this email if
I got to answer (like always) is only Justins mail adress, not the gromacs user list. I do it in cc<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> 14:59 Freitag, 13.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>> Hi<br>> <br>> I tried but I got an error. In my mol_in_water.pdb file all atoms of my molecule has the group notation ISO and all the water atoms has the group notation SOL. I used following command:<br>> <br>> g_select -f my mol_in_water.pdb -other -options -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'<br>> <br>> and I got the error:<br>> <br>> Invalid command line argument:<br>> -other<br>> <br>> How can I fix it.<br>> <br><br>Please see g_select -h for valid options. Mark was simply implying that you will likely need other command line options to make the program actually do something. Also note the space in your "my mol_in_water.pdb" will cause problems as well.<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>