<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span></span></div><div><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 size="2" face="Arial"> ----- Forwarded Message -----<br> <b><span style="font-weight:bold;">From:</span></b> dina dusti <dinadusti@yahoo.com><br> <b><span style="font-weight: bold;">To:</span></b> XAvier Periole <x.periole@rug.nl> <br> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday, April 10, 2012 10:44 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> martini coarse-grained<br> </font> </div> <br>
<meta http-equiv="x-dns-prefetch-control" content="off"><div id="yiv1652984297"><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;"><div><span>Thank you very much from your response. <br></span></div><div><span>I found the coordinate file of tiofen from PRODRG and I wrote .itp file for that according to definition of molecules in martini_v2.1_aminoacids.itp file.</span></div><div><span>What is your idea about this, Please?</span></div><div><br><span></span></div><div><span>Best Regards</span></div><div><span>Dina<br></span></div><div><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 size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> XAvier Periole <x.periole@rug.nl><br> <b><span
style="font-weight:bold;">To:</span></b> dina dusti <dinadusti@yahoo.com>;
Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight:bold;">Sent:</span></b> Tuesday, April 10, 2012 5:16 PM<br> <b><span style="font-weight:bold;">Subject:</span></b> Re: [gmx-users] martini coarse-grained<br> </font> </div> <br>
<div id="yiv1652984297"><div><div><br></div>Where did you find the topology?<div><br><div><div>On Apr 10, 2012, at 10:44 AM, dina dusti wrote:</div><br class="yiv1652984297Apple-interchange-newline"><blockquote type="cite"><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;"><div>Dear GROMACS Specialists,</div><div><br></div><div>I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please?</div><div>I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it right?</div><div>Or should I change SC5 to C-S-C for .gro file?</div><div>And my definition of tiofen in .itp file it is as followed , Please say me that is it right?<br></div><div><br></div><div>;;;;;; TIOFEN<br><br>[moleculetype]<br>; molname nrexcl<br> TIO
1<br><br>[atoms]<br>; id type resnr residu atom cgnr charge<br> 1 SC4 1 TIO SI1 1 0 <br> 2 SC5 1 TIO SI2 2 0 <br><br>[constraints]<br>; i j funct length<br> 1 2 1 0.27</div><div><br></div><div>Because I for benzene see a triangle in ngmx program, but for this see a line. Please help me to correction of mistakes.</div><div>Thank you very much in advance.</div><div><br></div><div>Best
Regards</div><div>Dina<br></div><div><br></div><div><br></div><div><br></div></div></div>-- <br>gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists</blockquote></div><br></div></div></div><br><br> </div> </div> </div></div></div><meta http-equiv="x-dns-prefetch-control" content="on"><br><br> </div> </div> </div></body></html>