<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>I still got the problem. What is wrong in this command:</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"'<br></div><div><br></div><div>In the pdb. file ISO is for the molecule and SOL for the water.<br></div><div><br></div><div>Please help</div><div><br></div><div>Greetings</div><div>Lara<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> Teemu Murtola <teemu.murtola@cbr.su.se><br> <b><span
style="font-weight: bold;">An:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Gesendet:</span></b> 18:20 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>On Fri, Apr 13, 2012 at 18:30, Lara Bunte <<a ymailto="mailto:lara.bunte@yahoo.de" href="mailto:lara.bunte@yahoo.de">lara.bunte@yahoo.de</a>> wrote:<br>> Is there no way only to use the .pdb file? How do I create from a .pdb a rtp<br>> file. With pdb2gmx and than grompp?<br><br>You can also provide a .pdb file to the -s option of g_select. And you<br>don't need to provide a -f file in that case if you simply want to<br>analyze the coordinates in a single configuration of that .pdb file.<br><br>Best regards,<br>Teemu<br>-- <br>gmx-users mailing list <a
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