MD Simulations and Force Field development

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.

[download from Google Drive] [download from our site]

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

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_PLAFF3GROMACS force field for PolyLactide simulations, files were prepared according to McAliley 2011 (dx.doi.org/10.1021/ct200251x).

[download from Google Drive] [download from our site]

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