Force Field Xrealspace.ManyBody(1)
Synopsis
realspace.ManyBody [-EhOTVz] [--bT] [--dee] [--oT] [--tR] [-a=0] [--bB=0.0] [--bC=1] [--bL=20.0] [--ch=<A>] [--clashThreshold=25.0] [--eR=none] [--fB=<finalBox>] [--fR=<final>] [--iB=<initialBox>] [--iC=<inclusionCutoff>] [--increment=3] [--iR=<interestedResidue>] [--kPH=0.0] [-L=2] [--lR=<list>] [--mC=-1] [--nB=3,3,3] [--pairClashThreshold=25.0] [--pH=0] [--pr=1] [--radius=2.0] [--sR=<start>] [--tC=3.0] [--thC=3. _ 0_] [--wA=1.0] [--window=7] [-X=<data> <data>]… files…
Options
- -h, --help
- Print command help and exit.
- -V, --version
- Print the Force Field X version and exit.
- --wA, --dataWeight=1.0
- The weight of the experimental data (wA).
- -X, --data=<data> <data>
- Specify input data filename and its weight (wA) (e.g. -X filename 1.0).
Many-Body Optimization Options
- -a, --algorithm=0
- Algorithm: default automatic settings (0), independent residues (1), all with rotamer elimination (2), all brute force (3), sliding window (4), or box optimization (5)
- --dee, --deadEnd
- Use dead-end elimination criteria instead of Goldstein criteria.
- -E, --decompose
- Print energy decomposition for the input structure (no optimization!).
- --eR, --energyRestart=none
- Load energy restart file from a previous run (requires that all parameters are the same).
- -L, --library=2
- Ponder and Richards (1) or Richardson (2) rotamer library.
- --mC, --monteCarlo=-1
- Follow elimination criteria with (n) Monte Carlo steps, or enumerate all remaining conformations, whichever is smaller.
- -O, --noOriginal
- Do not include starting coordinates as their own rotamer.
- --pH, --titrationPH=0
- Optimize the titration state of ASP, GLU, HIS and LYS residues at the given pH (pH = 0 turns off titration
- --tR, --titration
- Turn on titration state optimization
- -z, --revert
- Revert unfavorable changes.
Many-Body Box Optimization Options
- --bB, --boxBorderSize=0.0
- Extent of overlap between optimization boxes in Angstroms.
- --bC, --boxInclusionCriterion=1
- Criterion to use for adding a residue to a box: (1) uses C alpha only (N1/9 for nucleic acids), (2) uses any atom, and (3) uses any rotamer
- --bL, --approxBoxLength=20.0
- Approximate side lengths of boxes to be constructed (over-rides numXYZBoxes).
- --bT, --boxTitration
- Center boxes around titratable residues.
- --fB, --finalBox=<finalBox>
- Final box to optimize.
- --iB, --initialBox=<initialBox>
- Initial box to optimize.
- --nB, --numBoxes=3,3,3
- Specify number of boxes along X, Y, and Z (default: 3,3,3)
Many-Body Window Optimization Options
- --increment=3
- Sliding window increment.
- --window=7
- Size of the sliding window with respect to adjacent residues.
Many-Body Energy Expansion and Cut-off Options
- --clashThreshold=25.0
- The threshold for pruning clashes.
- --kPH, --pHRestraint=0.0
- Only allow titration state to change fromstandard state is self energy exceeds the restraint.
- --pairClashThreshold=25.0
- The threshold for pruning pair clashes.
- --pr, --prune=1
- Prune no clashes (0), only single clashes (1), or all clashes (2)
- --radius=2.0
- The sliding box and window cutoff radius (Angstroms).
- -T, --threeBody
- Include 3-Body interactions in the elimination criteria.
- --tC, --twoBodyCutoff=3.0
- Cutoff distance for two body interactions.
- --thC, --threeBodyCutoff=3.0
- Cutoff distance for three-body interactions.
Many-Body Residue Selection Options
- --ch, --chain=<A>
- Include only specified chain ID (default: all chains).
- --fR, --final=<final>
- Final residue to optimize (default: all residues).
- --iC, --inclusionCutoff=<inclusionCutoff>
- Distance which rotamers will be included when using only protons, titratable residues, or interested residue.
- --iR, --interestedResidue=<interestedResidue>
- Optimize rotamers within some distance of a specific residue.
- --lR, --listResidues=<list>
- Select a list of residues to optimize (eg. A11,A24,B40).
- --oT, --onlyTitration
- Rotamer optimize only titratable residues.
- --sR, --start=<start>
- Starting residue to optimize (default: all residues).