Hi Dina, Thiophen is a five-membered ring, like the histidine side-chain, which is modeled with three beads. And then you ought to choose the bead types such that they give good agreement with atomistic PMFs and/or partitioning of the same compound. It's very unlikely that just fiddling around a bit yields a suitable model.
Cheers, Tsjerk On Tue, Apr 10, 2012 at 8:29 PM, dina dusti <dinadu...@yahoo.com> wrote: > > ----- Forwarded Message ----- > From: dina dusti <dinadu...@yahoo.com> > To: XAvier Periole <x.peri...@rug.nl> > Sent: Tuesday, April 10, 2012 10:44 PM > Subject: martini coarse-grained > > Thank you very much from your response. > 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. > What is your idea about this, Please? > > Best Regards > Dina > > ________________________________ > From: XAvier Periole <x.peri...@rug.nl> > To: dina dusti <dinadu...@yahoo.com>; Discussion list for GROMACS users > <gmx-users@gromacs.org> > Sent: Tuesday, April 10, 2012 5:16 PM > Subject: Re: [gmx-users] martini coarse-grained > > > Where did you find the topology? > > On Apr 10, 2012, at 10:44 AM, dina dusti wrote: > > Dear GROMACS Specialists, > > I have doubt about definition of tiofen ring in MARTINI CG force field. May > I ask you to help me, Please? > I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it > right? > Or should I change SC5 to C-S-C for .gro file? > And my definition of tiofen in .itp file it is as followed , Please say me > that is it right? > > ;;;;;; TIOFEN > > [moleculetype] > ; molname nrexcl > TIO 1 > > [atoms] > ; id type resnr residu atom cgnr charge > 1 SC4 1 TIO SI1 1 0 > 2 SC5 1 TIO SI2 2 0 > > [constraints] > ; i j funct length > 1 2 1 0.27 > > Because I for benzene see a triangle in ngmx program, but for this see a > line. Please help me to correction of mistakes. > Thank you very much in advance. > > Best Regards > Dina > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
