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

[Mahsa E]

Thank you for your help!

Best regards,
Mahsa

On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul <jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
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>
>
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