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<div style="font-family:arial, helvetica, sans-serif;font-size:12pt;"><div>thanks felix<br>you are right.both exist.but how can i tell gromacs to put MG ions in the standard vicinity of ATP? or maybe gromacs knows it already and i have to just type "MG-ATP" instead of "ADP"?<br></div><div style="font-family:arial, helvetica, sans-serif;font-size:12pt;"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> "Rausch, Felix" <frausch@ipb-halle.de><br><b><span style="font-weight:bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight:bold;">Sent:</span></b> Wed, April 27, 2011 1:33:52 PM<br><b><span style="font-weight:bold;">Subject:</span></b> [gmx-users] MG-ATP<br></font><br>
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<div dir="ltr"><font color="#000000" face="Arial" size="2">Hi.</font></div>
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<div dir="ltr"><font color="#000000" face="Arial" size="2"><span>Looking at the list of building blocks available in GROMACS (<a target="_blank" href="http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks">http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks</a>) you can find ATP as well as MG. So having a ATP-MG-complex in your simulation shouldn't be a problem.</span></font></div>
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<div dir="ltr"><font face="Arial" size="2">Regards,</font></div>
<div dir="ltr"><font face="Arial" size="2">Felix</font></div></div>
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<font face="Tahoma" size="2"><b>Von:</b> gmx-users-bounces@gromacs.org im Auftrag von Sajad Ahrari<br><b>Gesendet:</b> Mi 27.04.2011 10:52<br><b>An:</b> gromacs user forum<br><b>Betreff:</b> [gmx-users] MG-ATP<br></font><br></div>
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<div style="font-size:12pt;color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;">dear users</div>
<div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="3">is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG, apart from each other and not being </font><font class="Apple-style-span" face="arial, helvetica, sans-serif">crystallized</font><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="3"> in the right place. can i omit them and replace ADP's with MG-ATP? or I should introduce this topology to gromacs?</font></div>
<div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="3">regards</font></div>
<div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="3">sajad </font></div>
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