<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi Mark <br>Sorry for the delayed reply. Somehow I missed your mail that time. <br>I am doing exactly what you have suggested. I am building up this missing part and then trying to run the simulation.<br>Again 'm sorry for this delay.<br>Best regards, <br>Abhik<br><br><div><div><div><font face="system" size="3"><strong>Abhik Mukhopadhyay<br> </strong></font></div><font size="3"><font size="3"><font size="2"><span style="font-weight: bold;"> Departamento Química / Faculdade de Ciências e Tecnologia </span><br style="font-weight: bold;"><span style="font-weight: bold;"> Universidade Nova de Lisboa , 2829-516 Caparica, Portugal </span><br style="font-weight: bold;"><span style="font-weight: bold;"></span></font></font><br>Mob. 00351912991251<br></font><font size="3"> <a rel="nofollow" target="_blank" href="http://xtal.dq.fct.unl.pt/">
http://xtal.dq.fct.unl.pt/</a><br></font><br></div></div><br><br>--- On <b>Fri, 3/13/09, Mark Abraham <i><Mark.Abraham@anu.edu.au></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">From: Mark Abraham <Mark.Abraham@anu.edu.au><br>Subject: Re: [gmx-users] problem in energy minimization<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Friday, March 13, 2009, 7:55 PM<br><br><pre>Abhik Mukhopadhyay wrote:<br>> Hi Jastin<br>> My pdb2gmx command line is<br>> pdb2gmx -ignh -f xx.pdb -o xxout.pdb -p xx.top -water spce<br>> <br>> When I created the topology it did not create a bond between those two<br>residues (between which the part is missing).<br><br>The above statement seems inconsistent with the observations below.<br><br>> > I am trying to run a simulation on a xray structure that has 15<br>residues<br>> missing. I
have made the topology file accordingly. But after energy<br>> minimization, the residues between which the portion is missing, got<br>connected.<br>> I tried an energy minimization with all-bonds constraint, but that i<br>guess did<br>> not do it properly.<br><br>By far the most likely reason for the residues that should be spaced by the 15<br>missing residues to "get connected" was that your topology had an<br>interaction defined.<br><br>The fact that these residues were missing from the X-ray structure doesn't<br>mean you should ignore their existence. Often they can be involved in useful<br>chemistry. I would most likely consider using some (non-GROMACS) modelling<br>software to "build in" such residues before attempting any MD.<br><br>There are alternatives which involve capping the pseudo-termini and possibly<br>using some kind of restraints, but these will be harder to defend to your<br>paper's
audience.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.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 www interface<br>or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></pre></blockquote></td></tr></table><br>