Frequently Asked Questions (FAQ)

How do I use the o2p?

  1. You need to obtein or generate a topology file for the oligomer, using (for example) SwissParam, Antechamber.

  2. Upload a oligomer coordinate file in Protein Data Bank (PDB) format (including all hydrogen atoms) and .itp file.

  3. View detail page and click Select Repeating Structure.

  4. This is repeating structure selector page. Click atoms which are ends of repeating structure.
    Selected atoms turn pink or green. When your selection is correct, click "do segm" button.
    The repeating structrue between selected atoms will trun blue (as defalut).

  5. Select repeating structure or end structrue then click white atom.
    The group atoms will change selected structrue color.

  6. After complete selection of atoms, you can get polymer fortamed topology and PDB file polymerization degree you set.
    Input the number of polymerization degree into Repeating count box and push Download button.
    If the simulation box needs ions or solvent, select from lists.
    Parameters of ions and solvents have not been pre-registered.
    You need to register parameters those ions or solvents.

How do I register the parameters of ions?

Upload following files from force field directory (each force field has its own directory).

To use new ions the force field does not contein, modify the same formated files then upload.

How do I register the parameters of solvents?

To use water solvent

This is an example for registration of tip3p model of charmm27 force field included Gromacs.

  1. Copy whole text of tip3p.itp to Topology file(.itp) textarea.

  2. Search matching rows with atomtypes described in tip3p.itp (OWT3 and HWT3) from atomtypes.atp.
    Then copy matched rows to atomtypes.atp textarea.

  3. Search matching rows with atomtypes described in tip3p.itp from ffnonbonded.itp.
    Matched rows are enclosed in #ifdef ~ #endif, so copy whole this area to ffnonbonded.itp textarea.

To use non-water solvent

This is an example for the case methanol.
You need to create .gro file not just parameters.
The .gro file must be named solvent.gro where solvent is the name you set as Solvent name.

  1. Change molecule name SOL in [ moleculetype ] section.
    Replace LIG with SOL in [ atoms ] secition.

  2. Copy [ moleculetype ] section and [ atoms ] section to Topology file(.itp) textarea.

  3. Extract atomtype and atomic mass from [ atomtypes ] seciton and fill atomtypes.atp textarea.

  4. Copy [ atomtypes ] section to ffnonbonded.itp textarea.
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