<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><br></span></div><div> Thanks for your reply.<br>But one more question: what about when the applied lipid bilayer is POPC? Is this .top file (topol_dppc) useful yet? How come?<br>You know, my main problem is that I don't know where this .top file come from?<br><br><span class="tab"></span></div><div>Sincerely,<br>Shima<br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Shima Arasteh <shima_arasteh2001@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org>
<br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, June 15, 2012 6:57 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Tutorial KALP-15 in DPPC<br> </font> </div> <br>
<br><br>On 6/15/12 10:25 AM, Shima Arasteh wrote:<br>><br>> Dear gmx users,<br>> I am doing KALP15 in DPPC following the Justin tutorial<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html<br>> . In the second step, the first command is grompp as follow:<br>><br>> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr<br>><br>> I want to know if the topol_dppc.top in this command is the .top file which produced by pdb2gmx at the beginning of the first step? If not, so what is that?<br>><br>><br><br>No, it is a different topology provided to you by the tutorial. Please note the <br>statements in the tutorial to this effect; it is the only time it is used.<br><br>-Justin<br><br>-- <br>========================================<br><br>Justin A. Lemkul, Ph.D.<br>Research Scientist<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg,
VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu/">vt.edu</a> | (540) 231-9080<br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br><br><br><br><br> </div> </div> </div></body></html>