<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">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 residues (between which the part is missing).<br><br>Thanks for your suggestion.<br>Abhik<br><br><div><div><div><font size="3" face="system"><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>Thu, 3/12/09, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] problem in energy minimization<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Thursday, March 12, 2009, 7:54 PM<br><br><pre><br>Abhik Mukhopadhyay wrote:<br>> Hi everyone,<br>> I am trying to run a simulation on a xray structure that has 15 residues<br>missing. I have made the topology file accordingly. But after energy<br>minimization, the residues between which the portion is missing, got connected.<br>I tried an energy minimization with all-bonds constraint, but that i guess did<br>not do it properly.<br>> This is the last part of the minimization run<br>> <br><br>When you created the
topology, did pdb2gmx add a bond between the residues<br>flanking the missing residues? What was your pdb2gmx command line?<br><br>If you are sure that the missing residues will not influence the dynamics<br>(think carefully!), then read in the manual about distance restraints. If you<br>have difficulties implementing these restraints, there are dozens of posts in<br>the list archive that should guide you in how to use them.<br><br>-Justin<br><br>> Stepsize too small, or no change in energy.<br>> Converged to machine precision,<br>> but not to the requested precision Fmax < 1000<br>> <br>> Double precision normally gives you higher accuracy.<br>> You might need to increase your constraint accuracy, or turn<br>> off constraints alltogether (set constraints = none in mdp file)<br>> <br>> writing lowest energy coordinates.<br>> <br>> Back Off! I just backed up ccpox_em.trr to ./#ccpox_em.trr.1#<br>> <br>> Back
Off! I just backed up ccpox_b4pr.pdb to ./#ccpox_b4pr.pdb.1#<br>> <br>> Steepest Descents converged to machine precision in 15 steps,<br>> but did not reach the requested Fmax < 1000.<br>> Potential Energy = -2.2785961e+05<br>> Maximum force = 5.1547680e+08 on atom 1004<br>> Norm of force = 8.2600877e+08<br>> <br>> My question is how can I run a simulation on these structure keeping that<br>part as it is?<br>> <br>> Thanking you in advance.<br>> Abhik<br>> <br>> <br>> <br>> <br>> *Abhik Mukhopadhyay<br>> *<br>> Departamento Química / Faculdade de Ciências e Tecnologia<br>> Universidade Nova de Lisboa , 2829-516 Caparica, Portugal<br>> <br>> Mob. 00351912991251<br>> http://xtal.dq.fct.unl.pt/<br>> <br>> <br>> <br>> ------------------------------------------------------------------------<br>> <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<br>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>-- ========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>ICTAS Doctoral Scholar<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://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<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></pre></blockquote></td></tr></table><br>