Project ID: plumID:22.024
Source: des/plumed.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
RESTARTActivate restart. More detailsMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=template.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-1830 # DEBUG DETAILED_TIMERSthe atoms that make up a molecule that you wish to align
# AB over backboneALPHABETA...Calculate the alpha beta CV More detailsATOMS1=the atoms involved for each of the torsions you wish to calculate@phi-100the four atoms that are required to calculate the phi dihedral for residue 100. Click here for more information.REFERENCE=pithe reference values for each of the torsional anglesATOMS2=the atoms involved for each of the torsions you wish to calculate@phi-101the four atoms that are required to calculate the phi dihedral for residue 101. Click here for more information.ATOMS3=the atoms involved for each of the torsions you wish to calculate@phi-102the four atoms that are required to calculate the phi dihedral for residue 102. Click here for more information.ATOMS4=the atoms involved for each of the torsions you wish to calculate@phi-103the four atoms that are required to calculate the phi dihedral for residue 103. Click here for more information.ATOMS5=the atoms involved for each of the torsions you wish to calculate@phi-104the four atoms that are required to calculate the phi dihedral for residue 104. Click here for more information.ATOMS6=the atoms involved for each of the torsions you wish to calculate@phi-105the four atoms that are required to calculate the phi dihedral for residue 105. Click here for more information.ATOMS7=the atoms involved for each of the torsions you wish to calculate@phi-106the four atoms that are required to calculate the phi dihedral for residue 106. Click here for more information.ATOMS8=the atoms involved for each of the torsions you wish to calculate@phi-107the four atoms that are required to calculate the phi dihedral for residue 107. Click here for more information.ATOMS9=the atoms involved for each of the torsions you wish to calculate@phi-108the four atoms that are required to calculate the phi dihedral for residue 108. Click here for more information.ATOMS10=the atoms involved for each of the torsions you wish to calculate@phi-109the four atoms that are required to calculate the phi dihedral for residue 109. Click here for more information.ATOMS11=the atoms involved for each of the torsions you wish to calculate@phi-110the four atoms that are required to calculate the phi dihedral for residue 110. Click here for more information.ATOMS12=the atoms involved for each of the torsions you wish to calculate@phi-111the four atoms that are required to calculate the phi dihedral for residue 111. Click here for more information.ATOMS13=the atoms involved for each of the torsions you wish to calculate@phi-112the four atoms that are required to calculate the phi dihedral for residue 112. Click here for more information.ATOMS14=the atoms involved for each of the torsions you wish to calculate@psi-100the four atoms that are required to calculate the psi dihedral for residue 100. Click here for more information.ATOMS15=the atoms involved for each of the torsions you wish to calculate@psi-101the four atoms that are required to calculate the psi dihedral for residue 101. Click here for more information.ATOMS16=the atoms involved for each of the torsions you wish to calculate@psi-102the four atoms that are required to calculate the psi dihedral for residue 102. Click here for more information.ATOMS17=the atoms involved for each of the torsions you wish to calculate@psi-103the four atoms that are required to calculate the psi dihedral for residue 103. Click here for more information.ATOMS18=the atoms involved for each of the torsions you wish to calculate@psi-104the four atoms that are required to calculate the psi dihedral for residue 104. Click here for more information.ATOMS19=the atoms involved for each of the torsions you wish to calculate@psi-105the four atoms that are required to calculate the psi dihedral for residue 105. Click here for more information.ATOMS20=the atoms involved for each of the torsions you wish to calculate@psi-106the four atoms that are required to calculate the psi dihedral for residue 106. Click here for more information.ATOMS21=the atoms involved for each of the torsions you wish to calculate@psi-107the four atoms that are required to calculate the psi dihedral for residue 107. Click here for more information.ATOMS22=the atoms involved for each of the torsions you wish to calculate@psi-108the four atoms that are required to calculate the psi dihedral for residue 108. Click here for more information.ATOMS23=the atoms involved for each of the torsions you wish to calculate@psi-109the four atoms that are required to calculate the psi dihedral for residue 109. Click here for more information.ATOMS24=the atoms involved for each of the torsions you wish to calculate@psi-110the four atoms that are required to calculate the psi dihedral for residue 110. Click here for more information.ATOMS25=the atoms involved for each of the torsions you wish to calculate@psi-111the four atoms that are required to calculate the psi dihedral for residue 111. Click here for more information.ATOMS26=the atoms involved for each of the torsions you wish to calculate@psi-112the four atoms that are required to calculate the psi dihedral for residue 112. Click here for more information.LABEL=abbb ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# AB over sidechainsALPHABETA...Calculate the alpha beta CV More detailsATOMS1=the atoms involved for each of the torsions you wish to calculate@chi1-101the four atoms that are required to calculate the chi1 dihedral for residue 101. Click here for more information.REFERENCE=pithe reference values for each of the torsional anglesATOMS2=the atoms involved for each of the torsions you wish to calculate@chi1-102the four atoms that are required to calculate the chi1 dihedral for residue 102. Click here for more information.ATOMS3=the atoms involved for each of the torsions you wish to calculate@chi1-103the four atoms that are required to calculate the chi1 dihedral for residue 103. Click here for more information.ATOMS4=the atoms involved for each of the torsions you wish to calculate@chi1-105the four atoms that are required to calculate the chi1 dihedral for residue 105. Click here for more information.ATOMS5=the atoms involved for each of the torsions you wish to calculate@chi1-107the four atoms that are required to calculate the chi1 dihedral for residue 107. Click here for more information.ATOMS6=the atoms involved for each of the torsions you wish to calculate@chi1-109the four atoms that are required to calculate the chi1 dihedral for residue 109. Click here for more information.ATOMS7=the atoms involved for each of the torsions you wish to calculate@chi1-110the four atoms that are required to calculate the chi1 dihedral for residue 110. Click here for more information.ATOMS8=the atoms involved for each of the torsions you wish to calculate@chi1-111the four atoms that are required to calculate the chi1 dihedral for residue 111. Click here for more information.LABEL=absc ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# Alpha-helix for CDR helix:ALPHARMSDProbe the alpha helical content of a protein structure. More detailsRESIDUES=102-112this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=DRMSDthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure type
# Beta-sheet for CDR # para: PARABETARMSD RESIDUES=100-112 TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} anti:ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More detailsRESIDUES=102-112this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=DRMSDthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure type
# Beta-sheet for C-terminus # ctanti: ANTIBETARMSD RESIDUES=94-102,112-120 TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}
# Global CDR dihedral # dih: TORSION ATOMS=1493,1486,1656,1646
#PBMETAD ... # LABEL=pbmetad # ARG=abbb,absc,helix.lessthan,anti.lessthan,dih # PACE=500 HEIGHT=1.2 BIASFACTOR=24 WALKERS_MPI # SIGMA=1.5,0.5,2.0,1.5,0.3 # FILE=HILLS_abbb,HILLS_absc,HILLS_helix,HILLS_anti,HILLS_dih # GRID_MIN=-1,-1,-1,-1,-pi # GRID_MAX=28,10,38,30,pi # GRID_WFILES=GRID_abbb,GRID_absc,GRID_helix,GRID_anti,GRID_dih # GRID_WSTRIDE=10000 #... PBMETADPBMETAD...Used to performed Parallel Bias metadynamics. More detailsLABEL=pbmetada label for the action so that its output can be referenced in the input to other actionsARG=abbb,absc,helix.lessthan,anti.lessthanthe input for this action is the scalar output from one or more other actionsPACE=500the frequency for hill addition, one for all biasesHEIGHT=1.2the height of the Gaussian hills, one for all biasesBIASFACTOR=24use well tempered metadynamics with this bias factor, one for all biasesWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRSIGMA=1.5,0.5,2.0,1.5the widths of the Gaussian hillsFILE=HILLS_abbb,HILLS_absc,HILLS_helix,HILLS_antifiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundGRID_MIN=-1,-1,-1,-1the lower bounds for the gridGRID_MAX=28,10,38,30the upper bounds for the gridGRID_WFILES=GRID_abbb,GRID_absc,GRID_helix,GRID_anti # GRID_RFILES=GRID_abbb,GRID_absc,GRID_helix,GRID_antidump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILESGRID_WSTRIDE=10000 ... PBMETADfrequency for dumping the gridPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=BIASthe name of the file on which to output these quantitiesARG=abbb,absc,helix.lessthan,anti.lessthan,pbmetad.biasthe input for this action is the scalar output from one or more other actions