<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Tsjerk,</span></div><div><span><br></span></div><div><span>Thank you very much from your response.</span></div><div><span>OK, it means that I should select SC4, SC4 and SC5 for tiophen (SC4s = C-C and SC5 = S)?</span></div><div><span>On the other hand, I have 2 other structure, aniline and pyrrole. If I select three beads for both of them consist of SC4, SC4 and SP1, consequently, they become similar together!!!</span></div><div>Please help me.</div><div><br></div><div>Thank you very much again.</div><div>Best Regards</div><div>Dina<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> Tsjerk Wassenaar <tsjerkw@gmail.com><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 11:38 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] martini coarse-grained<br> </font> </div> <br>
Hi Dina,<br><br>Thiophen is a five-membered ring, like the histidine side-chain, which<br>is modeled with three beads. And then you ought to choose the bead<br>types such that they give good agreement with atomistic PMFs and/or<br>partitioning of the same compound. It's very unlikely that just<br>fiddling around a bit yields a suitable model.<br><br>Cheers,<br><br>Tsjerk<br><br><br>On Tue, Apr 10, 2012 at 8:29 PM, dina dusti <<a ymailto="mailto:dinadusti@yahoo.com" href="mailto:dinadusti@yahoo.com">dinadusti@yahoo.com</a>> wrote:<br>><br>> ----- Forwarded Message -----<br>> From: dina dusti <<a ymailto="mailto:dinadusti@yahoo.com" href="mailto:dinadusti@yahoo.com">dinadusti@yahoo.com</a>><br>> To: XAvier Periole <<a ymailto="mailto:x.periole@rug.nl" href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>> Sent: Tuesday, April 10, 2012 10:44 PM<br>> Subject: martini coarse-grained<br>><br>> Thank you very much
from your response.<br>> I found the coordinate file of tiofen from PRODRG and I wrote .itp file for<br>> that according to definition of molecules in martini_v2.1_aminoacids.itp<br>> file.<br>> What is your idea about this, Please?<br>><br>> Best Regards<br>> Dina<br>><br>> ________________________________<br>> From: XAvier Periole <<a ymailto="mailto:x.periole@rug.nl" href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>> To: dina dusti <<a ymailto="mailto:dinadusti@yahoo.com" href="mailto:dinadusti@yahoo.com">dinadusti@yahoo.com</a>>; Discussion list for GROMACS users<br>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Tuesday, April 10, 2012 5:16 PM<br>> Subject: Re: [gmx-users] martini coarse-grained<br>><br>><br>> Where did you find the topology?<br>><br>> On Apr 10, 2012, at 10:44 AM, dina dusti
wrote:<br>><br>> Dear GROMACS Specialists,<br>><br>> I have doubt about definition of tiofen ring in MARTINI CG force field. May<br>> I ask you to help me, Please?<br>> I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it<br>> right?<br>> Or should I change SC5 to C-S-C for .gro file?<br>> And my definition of tiofen in .itp file it is as followed , Please say me<br>> that is it right?<br>><br>> ;;;;;; 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<br>><br>> Because I for benzene see a triangle in ngmx program, but for this see a<br>> line. Please help me to correction of mistakes.<br>> Thank you very much in advance.<br>><br>> Best Regards<br>> Dina<br>><br>><br>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" 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<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>><br>><br>><br>><br>><br>><br>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto: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<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br><br><br> </div> </div> </div></body></html>