OK. I have a protein "ab" and ligand "lig", and I want to select the bound water between them. So I used<br><br>g_select -f trajout.xtc -s mdrun.tpr -n index.ndx -select '"boundwaters" resname SOL and within 0.4 of group "ab" and within 0.4 of group "lig"' -on boundwaters.ndx<br>
<br>Then I can use the ndx file to do other things. The hard part is what after -select <br><br><br><div class="gmail_quote">On Mon, Apr 2, 2012 at 5:11 PM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span> wrote:<br>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">For future reference of others that may struggle with g_select, it would be a very good idea for you to put on the emailing list how you achieved it.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Catch ya,<br>
<br>
Dr. Dallas Warren<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Medicinal Chemistry and Drug Action<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a href="tel:%2B61%203%209903%209304" value="+61399039304" target="_blank">+61 3 9903 9304</a><br>
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When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>Yun Shi<br>
<b>Sent:</b> Tuesday, 3 April 2012 9:58 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] Re: how to g_select bound water molecules<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Never mind. I got it.<u></u><u></u></p>
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<p class="MsoNormal">On Mon, Apr 2, 2012 at 4:20 PM, Yun Shi <<a href="mailto:yunshi09@gmail.com" target="_blank">yunshi09@gmail.com</a>> wrote:<u></u><u></u></p>
<p class="MsoNormal">Hello all,<br>
<br>
Can anyone tell me how to get in "help examples" in g_select by typing some commands?<br>
<br>
Anyway, I want to select bound waters between my ligand and protein using -select 'resname SOL & within 0.5 ...'. Any idea?<br>
<br>
Thanks for any suggestion.<span style="color:#888888"><br>
<br>
<span>Yun</span></span><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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