Also, I forgot to mention that I need to throw a protein into the mix. How would I get both the protein and the DPC into the box?
On Tue, July 12, 2011 10:46 am, Justin A. Lemkul wrote: > > > Janowicz, Adrianna C. wrote: >> Users, >> I'm trying to start a micelle modeling project & have tried countless >> approaches to making a DPC micelle. My problems include: >> -DPC not being recognized when I try to imput it into the [molecules] >> seciton of the topology file to account for the DPC molecules in the >> water >> topology. Otherwise, the molecule #s do not match. (This approach >> included >> using a coordinate file for DPC & using the -nmol fuction in genbox to >> place the DPC molecules into the water). >> >> I would appreciate any help. Even if this means taking a totally >> different >> approach in getting the DPC molecules into the box. >> > > The best approach would be to: > > 1. Create the topology for a single molecule of DPC > 2. Generate a configuration of the DPC micelle and edit the number of > molecules > in the .top appropriately > 3. Solvate and let genbox add the correct number of water molecules to the > .top > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
