On 2012-12-19 10:16:09AM +0530, Archana Sonawani wrote: > Hi, > > I want to simulate a peptide using SDS micelle. The peptide is random > coil, > but I want it to be helical; therefore, I will use TFE for inducing > helix.
You use TFE in a wet lab to physically induce helicity in real life. For a simulation, there is no guarantee that the forcefield you are using will behave in the same way. Might as well just use distance restraints to force the helicity. > I have never performed simulations using micelle. I have following > queries: > 1. *From where would I get coordinates of SDS micelle-water complex? *( > I > have .itp file for SDS) the g_membed introduciton page has an example of embedding in a POPE micelle. http://wwwuser.gwdg.de/~ggroenh/membed.html You can probably conduct a literature search and find a paper that provides a pdb for an SDS micelle. > 2. Do I require lipid.itp for this simulation? you say you already have a .itp for SDS that works your chosen forcefield? -- 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
