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

Mahsa E ebadi.mahsa at gmail.com
Mon Aug 7 02:36:17 CEST 2017

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).

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)?

 Your kind help on this is very much appreciated.

Best regards,

On Sun, Aug 6, 2017 at 2:34 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 8/5/17 8:12 AM, Mahsa E wrote:
>> Dear gmx-users,
>> I am trying to build a polymer box from scratch and generate the required
>> input files. So far, I did these steps:
>> 1. built a chain of the polymer
>> 2. run ACPYPE to generate the topology file...
>> However, since the chain is long, it took so long time with ACPYPE and the
>> calculation is timed out without convergence.
>> - Is it possible to restart the ACPYPE calculation?
>> I read in some tutorials that it is also possible to run the ACPYPE
>> calculations for the monomeric unit instead and repeat its parameters for
>> the whole chain. How is it possible? The polymer chain may have a
>> conformation with different angles and dihedrals than in the monomer.
>> In general, how can I use the topology file of a monomer for the longer
>> chain of a polymer ?
>> Could you please advise me?
> You parametrize the monomer (charges, atom types, bonded parameters), then
> build up by doing, e.g. conformational energy scans of dihedral rotations
> between the dimer.  That way you can build a proper model of the whole
> polymer.  Do not try to parametrize an entire polymer at once; you'll end
> up with a conformation-specific solution for a given geometry, if you can
> even get it to work at all.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> ==================================================
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