Thank you for your help! Best regards, Mahsa
On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/6/17 8:35 PM, Mahsa E wrote: > >> Hello Justin, >> >> Thank you so much for your reply! >> >> I followed what you suggested. Please correct me if I misunderstood; >> >> 1- I used acpype to generate the parameters (charges, atom types, and >> bonded parameters) for the monomer, which create many files including >> GMX_OPLS.itp , GMX_OPLS.top and GMX.gro files. >> >> 2- Then I build the dimer and used the conformer search in Marvin/Avogadro >> to find the best conformer for the dimer (.xyz or .pdb). >> >> > You'll need to parametrize (at minimum) dihedral terms around the bond > connecting the monomers in the dimer. Finding a single conformer doesn't > give you that information. You need to back up and consult the primary > literature for how your force field should work and how things should be > parametrized (right level of theory, expected level of agreement, etc). > This is not something that either acepype or GROMACS are going to give you; > it usually requires QM work and parameter fitting. > > 3- The missing part for me is from this step. What should I do after >> running acpype for the dimer ? >> how to use the information from previous steps to generate the .itp file >> for a longer chain of polymer (like 25 units)? >> >> > If you've parametrized all possible internal parameters in small model > systems, there's nothing special about larger ones; they're just small > model compounds linked together, so you've already done everything. Just > use pdb2gmx with suitable .rtp files: > > http://www.gromacs.org/Documentation/How-tos/Polymers > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.