Current version: ff-nucleic-OL15
ff-nucleic-OL15 force field is ff99bsc0 plus the following Olomouc dihedral refinements:
| DNA | ||
|---|---|---|
| χOL4 | refinement of DNA glycosidic torsion chi | [6] |
| εζOL1 | refinement of eps/zeta torsions | [7] |
| βOL1 | refinement of beta torsion | [8] |
| RNA | ||
| χOL3 | correction for RNA glycosidic torsion chi | [4,5] |
AMBER:
Parameters can be used in AMBER 16 by sourcing files in tLeaP: leaprc.RNA.OL3, leaprc.DNA.OL15
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Alternatively, ff-nucleic-OL15 may be downloaded here
Parameters may be read into tLEaP using command: tleap -s -f leap-ff-nucleic-OL15.in
Files are prepared for use with AMBER 14. Note that all downloaded files should be placed in the current directory (from which tLEaP was launched) or you should define the path to these in leap-ff-nucleic-OL15.in
GROMACS:
amber14sb_OL15.ff package may be downloaded here
For more information about implementation and validation, see here
Alternatively, topologies can be prepared by LEaP (AmberTools) and then converted to GROMACS format by ACPYPE.
Latest version (still in testing): OL21 DNA force Field
OL21 DNA force field may be downloaded here
Parameters may be read into tLEaP using command: tleap -s -f leap-ff-nucleic-OL21.in
Files are prepared for use with AMBER 16. Note that all downloaded files should be placed in the current directory (from which tLEaP was launched) or you should define the path to these in leap-ff-nucleic-OL21.in
Previous versions:
ff99bsc0εζOL1χOL4 parameters for DNA are available in the Amber simulation package since Amber 14 (only in version downloaded after April 2015) and also may be downloaded here.
ff99bsc0χOL3 combination for RNA is present in the ff10, ff12SB and ff14SB force fields and is assigned by default by AmberTools 1.5 and later with its LEaP based tools. Port for GROMACS by Giovanni Bussi is available here.
