[gmx-users] Generating topology file for a long polymer chain

Justin Lemkul jalemkul at vt.edu
Mon Aug 7 16:35:35 CEST 2017

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:




Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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