<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br><br>--- On <b>Mon, 27/7/09, Morteza Khabiri <i><khabiri@greentech.cz></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Morteza Khabiri <khabiri@greentech.cz><br>Subject: [gmx-users] POSITION-RESTRAIN<br>To: gmx-users@gromacs.org<br>Date: Monday, 27 July, 2009, 7:35 PM<br><br><div class="plainMail">Dear gmxusers.<br><br>I want to restrain the lipids in my system which contains protein,lipid<br>and water. I make the restraint itp file by genpr then I added it in<br>toplogy file.<br>After doing grompp to make tpr file I get the following message:<br><br>Fatal error:<br>[ file "posre_entirelipid1.itp", line 56 ]:<br> Atom index (53) in position_restraints out of bounds (1-52)<br>I found the similar error in the mailing
list and they suggested probably<br>the place of restraint itp file which was included in topology file is<br>wrong. However, I tried several positions for restraint itp but I think<br>it is not the<br>solution. Do you have any other suggestion about this problem??????<br><br>Thanks<br><br><br>hi, <br>Mark is right.....the position restrain.itp file should be included in your topology file in the proper place otherwise the problem would continue. place the .itp file after the section <br><font face="Arial"><font size="3"><font size="-1" face="courier">; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br><br>best wishes <br>Shamik<br></font></font></font><br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote></td></tr></table><br>
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