• Download ffparmbc0.tar.gz
• Installation: Just put files in working directory and use with pdb2gmx -ff test

If you use these files please cite:

• Reshetnikov, R ; Golovin, A ; Spiridonova, V ; Kopylov, A ; Sponer, J. Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations. (2010). JOURNAL OF CHEMICAL THEORY AND COMPUTATION, Volume: 6, Issue: 10, Pages: 3003-3014

• Reference in BibTex format
• Reference in EndNote format

• Download parmbsc0.ff.tar.gz
• Installation: Just put folder parmbc0.ff in working directory and use with pdb2gmx -ff parmbc0

If you use these files please cite:

• Reshetnikov, RV, Sponer, J, Rassokhina, OI, Kopylov, AM, Tsvetkov, PO, Makarov, AA, Golovin, AV. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process. (2011). NUCLEIC ACIDS RESEARCH Volume: 39 Issue: 22 Pages: 9789-9802

DOI: 10.1093/nar/gkr639

• Reference in BibTex format
• Reference in EndNote format

Files of parmbc0 forcefield for Gromacs 3.x - 4.0.7

If you use these files please cite:

• Reshetnikov, R ; Golovin, A ; Spiridonova, V ; Kopylov, A ; Sponer, J. Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations. (2010). JOURNAL OF CHEMICAL THEORY AND COMPUTATION, Volume: 6, Issue: 10, Pages: 3003-3014 DOI: 10.1021/ct100253m

Reference in BibTex format/Reference in EndNote format

Files of parmbc0 forcefield for Gromacs 4.5.x

If you use these files please cite:

• Reshetnikov, RV, Sponer, J, Rassokhina, OI, Kopylov, AM, Tsvetkov, PO, Makarov, AA, Golovin, AV. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process. (2011). NUCLEIC ACIDS RESEARCH Volume: 39 Issue: 22 Pages: 9789-9802 DOI: 10.1093/nar/gkr639

Reference in BibTex format/Reference in EndNote format

-- AndreyGolovin - 2012-04-18

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