FORCE FIELD FILES
Here we present PARMBSC1, a force field for DNA refined from high-level QM calculations (up to CBS-CCSD(T)) in the gas phase and in solution (SCRF-MST), which provides an improved representation of sugar puckering, ε, ζ and χ torsions.
The force field was tested for more than 3 years in nearly 100 different DNA systems (~140 microseconds of aggregated simulation time). The results obtained are of unprecedented quality and open up new frontiers for the simulation of DNA. All simulations done to validate the force field are available for free download at the BIGNASim database.
The PARMBSC1 parameters files are available from the Dans Lab. website, from the MMB website, and are also included in state-of-the-art MD simulation packages like AMBER or GROMACS.
We also provide (at your own risk), the preliminary parameters for 5-methyl-cytosine, and 5-hydroxymethyl-cytosine compatibles with PARMBSC1.
(not published yet, in post-validation stage)
PARMBSC1
PARMBSC1 parameters include a library file (.lib) and a frcmod file (.frcmod) that could be directly loaded into the LEAP program of AMBERTOOLS (free).
For its use on the GROMACS program, we highly recommend the native porting done by the group of Berg Hess
5mC and 5hmC
Parameters for the epigenetically modified nucleobases include a library file (.lib) and a frcmod file (.frcmod) that could be directly loaded into the LEAP program of AMBERTOOLS (free).
The developed parameters were designed to work with the PARMBSC1 force field.