Download Chitosan Force Field GROMOS 56ACARBO_CHT for GROMACS molecular dynamic simulations
GROMOS 56ACARBO_CHT — new GROMACS force field for simulations chitin, chitosan and its N-substituted derivatives.
Citation: Naumov, V.S. & Ignatov, S.K. Modification of 56ACARBO force field for molecular dynamic calculations of chitosan and its derivatives // J Mol Model (2017) 23: 244. https://doi.org/10.1007/s00894-017‑3421-x (DOWNLOAD PDF)
To create chitosan topology using pdb2gmx and GROMOS 56ACARBO_CHT:
1. Download and setup force field 56ACARBO_CHT
2. Create gro-file with necessary structure of chitosan (example). Chitosan should consist of residues: CHT, CHT0, CHTN, CHTP, CHTR and ACE2 (for details please see our article, also attached). Gro file also could include any other molecules. The only restriction is compatibility with 56ACARBO_CHT force filed (the correct names for residues and atoms).
3. Run pdb2gmx with created gro-file and get topol.top wich contains topology, excepted some special interactions for chitosan molecules.
4. Run python-script with topol.top and get top_new.top. Script adds interactions that pdb2gmx does not support. So, top_new.top contains full topology.
Download PolyLactide Force Field OPLS PLAFF3 for GROMACS molecular dynamic simulations
OPLSAA_PLAFF3 — GROMACS force field for PolyLactide simulations, files were prepared according to McAliley 2011 (dx.doi.org/10.1021/ct200251x).
Download tiorg-smooth Slater-Koster files for DFTB calculations
The original tiorg parameter set (http://www.dftb.org/parameters/download/tiorg/tiorg-0–1-cc/) was modified by re-splining in order to escape unphysical vibratioal frequencies.