<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Hi,</DIV>
<DIV>I want to&nbsp;couple gromacs and orca.&nbsp;I saw ORCA&nbsp;interface is written by <A class=list title="Search for commits authored by Gerrit Groenhof" href="http://repo.or.cz/w/gromacs.git/search/04a7eac128bc022344b5bc9a7f255deaa0bcab19?s=Gerrit+Groenhof;st=author">Gerrit Groenhof</A>.</DIV>
<DIV>How do I&nbsp;install ORCA interface with ORCA and GROMACS?&nbsp;&nbsp;<BR><BR>Farzad Molani,<BR>Ph.D Student,<BR>Department of Theoretical Chemistry and Biochemistry,<BR>K. N. Toosi University of Technology,<BR>Tehran, Iran.<BR>Tel.: 009821 2306 4280 <BR>Fax: 009821 2285 3650 <BR>Web: http://www.kntu.ac.ir<BR><BR>--- On <B>Sat, 11/21/09, Mark Abraham <I>&lt;Mark.Abraham@anu.edu.au&gt;</I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Mark Abraham &lt;Mark.Abraham@anu.edu.au&gt;<BR>Subject: Re: [gmx-users] access code for qmmm<BR>To: "Discussion list for GROMACS users" &lt;gmx-users@gromacs.org&gt;<BR>Date: Saturday, November 21, 2009, 4:45 PM<BR><BR>
<DIV class=plainMail>Farzad Molani wrote:<BR>&gt; Hi,<BR>&gt; I saw web page for ORCA, and I saw an access code for QM/MM ORCA interface, but I do'nt know, how do I can install. please guide me. <BR><BR>What's the problem? Google for the home pages and follow the instructions there.<BR><BR>Mark<BR><BR>&gt; --- On *Tue, 11/17/09, <A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" ymailto="mailto:ilona.baldus@bioquant.uni-heidelberg.de">ilona.baldus@bioquant.uni-heidelberg.de</A> /&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" ymailto="mailto:ilona.baldus@bioquant.uni-heidelberg.de">ilona.baldus@bioquant.uni-heidelberg.de</A>&gt;/* wrote:<BR>&gt; <BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;From: <A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de"
 ymailto="mailto:ilona.baldus@bioquant.uni-heidelberg.de">ilona.baldus@bioquant.uni-heidelberg.de</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" ymailto="mailto:ilona.baldus@bioquant.uni-heidelberg.de">ilona.baldus@bioquant.uni-heidelberg.de</A>&gt;<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Subject: Re: [gmx-users] access code for qmmm<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;To: <A href="http://us.mc557.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Date: Tuesday, November 17, 2009, 5:29 PM<BR>&gt; <BR>&gt; <BR>&gt; <BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Orca is free for example. Apparently, there's an implementation for<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Gromacs.<BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Please send flowers and chocolate directely to Villa Bosch, where I<BR>&gt;&nbsp;
 &nbsp;&nbsp;&nbsp;am working. You find the adress on the internet ;)<BR>&gt; <BR>&gt; <BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Quoting Farzad Molani &lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=farzad_c81@yahoo.com" ymailto="mailto:farzad_c81@yahoo.com">farzad_c81@yahoo.com</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=farzad_c81@yahoo.com" target=_blank>http://us.mc557.mail.yahoo.com/mc/compose?to=farzad_c81@yahoo.com</A>&gt;&gt;:<BR>&gt; <BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Hi Ilona,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; I saw the web adress. unfortunetly we don't have gaussian and<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;gamess&nbsp; uk. I want to calculate QM region by ab inition or DFT<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;methods.&nbsp; which quantum mechanic package do I use?&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Farzad Molani,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Ph.D Student,<BR>&gt;&nbsp;
 &nbsp; &nbsp; &gt; Department of Theoretical Chemistry and Biochemistry,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; K. N. Toosi University of Technology,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Tehran, Iran.<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Tel.: 009821 2306 4280<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Fax: 009821 2285 3650<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Web: <A href="http://www.kntu.ac.ir/" target=_blank>http://www.kntu.ac.ir</A> &lt;<A href="http://www.kntu.ac.ir/" target=_blank>http://www.kntu.ac.ir/</A>&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; --- On Mon, 11/16/09, <A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" ymailto="mailto:ilona.baldus@bioquant.uni-heidelberg.de">ilona.baldus@bioquant.uni-heidelberg.de</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de"
 target=_blank>http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de</A>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" ymailto="mailto:ilona.baldus@bioquant.uni-heidelberg.de">ilona.baldus@bioquant.uni-heidelberg.de</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" target=_blank>http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de</A>&gt;&gt;<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;wrote:<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; From: <A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" ymailto="mailto:ilona.baldus@bioquant.uni-heidelberg.de">ilona.baldus@bioquant.uni-heidelberg.de</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A
 href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" target=_blank>http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de</A>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" ymailto="mailto:ilona.baldus@bioquant.uni-heidelberg.de">ilona.baldus@bioquant.uni-heidelberg.de</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de" target=_blank>http://us.mc557.mail.yahoo.com/mc/compose?to=ilona.baldus@bioquant.uni-heidelberg.de</A>&gt;&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Subject: Re: [gmx-users] access code for qmmm<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; To: <A href="http://us.mc557.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A
 href="http://us.mc557.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://us.mc557.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org</A>&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Date: Monday, November 16, 2009, 9:05 PM<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Hi Farzad,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; I neither installed nor compiled Gaussian so far but actually, I<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;am&nbsp; intending to do so in near future. I found this link:<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; <A href="http://wwwuser.gwdg.de/~ggroenh/qmmm.html#doc" target=_blank>http://wwwuser.gwdg.de/~ggroenh/qmmm.html#doc</A><BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; (scroll down to Gaussian03)<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Cheers,
 Ilona<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Quoting Farzad Molani &lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=farzad_c81@yahoo.com" ymailto="mailto:farzad_c81@yahoo.com">farzad_c81@yahoo.com</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=farzad_c81@yahoo.com" target=_blank>http://us.mc557.mail.yahoo.com/mc/compose?to=farzad_c81@yahoo.com</A>&gt;&gt;:<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Hello,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; I'm going to study reactions mechanism for enzymes. I want to<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;use gromacs<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; for qmmm calculations. I read Gerrit Groenhof's access code<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;for&nbsp;&nbsp;&nbsp;qmmm. I have some questions about Groenhof's
 code:<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; 1- After compileing this code,Does QM package (for example&nbsp; &nbsp;&nbsp;&nbsp;Gaussian&nbsp; 03) need to modify ?<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; 2- Does this code implement in Gromacs 4.0?<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Thanks in advance.<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Farzad Molani,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Ph.D Student,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Department of Theoretical Chemistry and Biochemistry,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; K. N. Toosi University of Technology,<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Tehran, Iran.<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Tel.: 009821 2306 4280=20<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Fax: 009821 2285 3650=20<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt; Web: <A href="http://www.kntu.ac.ir/" target=_blank>http://www.kntu.ac.ir</A> &lt;<A href="http://www.kntu.ac.ir/"
 target=_blank>http://www.kntu.ac.ir/</A>&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; --<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; gmx-users mailing list&nbsp; &nbsp; <A href="http://us.mc557.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc557.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://us.mc557.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org</A>&gt;<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; <A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Please search the archive at <A href="http://www.gromacs.org/search"
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