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Thank you for your reply, <br><br>I have been using [ position_restraints ], I do not know why it came out that way in the mail. <br>I agree with you, the problem probably comes from the position the code lies in inside the .top file. I put it at the end of the file because I thought that was the way it was supposed to be done. Perhaps this is incorrect. <br><br>The final lines of the .top file are: <br><br>Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>Protein<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br><br>[ position_restraints ]<br>2 1 1000 0 1000 ;<br>3 1 1000 0 1000 ;<br>4 1 1000 0 1000 ;<br>5 1 1000 0 1000 ;<br>6 1 1000 0 1000 ;<br>7 1 1000 0 1000 ;<br>8 1 1000 0 1000 ;<br>9 1 1000 0 1000 ;<br><br> <br><br>> Date: Thu, 3 Jun 2010 09:00:36 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] position restraints<br>> <br>> <br>> <br>> abdullah ahmed wrote:<br>> > Hello,<br>> > <br>> > I would like to restrain my molecule to a specific position in space. I <br>> > would like for certain atoms to lie on the y-axis. To do this I used <br>> > the following code/lines in my .top file:<br>> > <br>> > [ position restraints ]<br>> <br>> This is an incorrect directive. It should be position_restraints.<br>> <br>> > 2 1 1000 0 1000 ;<br>> > 3 1 1000 0 1000 ;<br>> > 4 1 1000 0 1000 ;<br>> > 5 1 1000 0 1000 ;<br>> > 6 1 1000 0 1000 ;<br>> > 7 1 1000 0 1000 ;<br>> > 8 1 1000 0 1000 ;<br>> > 9 1 1000 0 1000 ;<br>> > <br>> > Unfortunately, after minimization my file contained the molecule in the <br>> > same position as when the restraints were not applied.<br>> > <br>> > Does anyone know what I am doing wrong?<br>> > <br>> <br>> Perhaps the directive name is an issue, although I think grompp should have <br>> raised a warning of some sort. Otherwise, is this block within the appropriate <br>> [moleculetype] in the topology? Is it under control of an #ifdef block that you <br>> haven't invoked in the .mdp file?<br>> <br>> -Justin<br>> <br>> > Thanks in advance,<br>> > Abdullah<br>> > <br>> > ------------------------------------------------------------------------<br>> > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up <br>> > now. <https://signup.live.com/signup.aspx?id=60969><br>> > <br>> <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>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br><hr>Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. <a href="https://signup.live.com/signup.aspx?id=60969">Sign up now.</a> <br /><hr />Hotmail: Powerful Free email with security by Microsoft. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Get it now.</a></body>
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