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.
