bfee2 2.5.0__py3-none-any.whl

BFEE2/templates_gromacs/001.colvars.template

@@ -0,0 +1,76 @@
+colvarsTrajFrequency    500
+colvarsRestartFrequency 50000
+indexFile               colvars.ndx
+
+colvar {
+    name                    RMSD
+    width                   $rmsd_bin_width
+    lowerboundary           $rmsd_lower_boundary
+    upperboundary           $rmsd_upper_boundary
+    subtractAppliedForce    on
+    extendedLagrangian      on
+    extendedFluctuation     $rmsd_bin_width
+    rmsd {
+        atoms {
+            indexGroup $ligand_selection
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+harmonicWalls {
+    colvars             RMSD
+    lowerWalls          $rmsd_lower_boundary
+    upperWalls          $rmsd_upper_boundary
+    lowerWallConstant   $rmsd_wall_constant
+    upperWallConstant   $rmsd_wall_constant
+}
+
+abf {
+    colvars             RMSD
+    FullSamples         10000
+    historyfreq         50000
+    writeCZARwindowFile on
+}
+
+metadynamics {
+    colvars             RMSD
+    hillWidth           $rmsd_bin_width
+    hillWeight          0.2092
+    wellTempered        on
+    biasTemperature     4000
+}
+
+colvar {
+    name translation
+    distance {
+        group1 {
+            indexGroup $protein_selection
+        }
+        group2 {
+            dummyAtom $protein_center
+        }
+    }
+}
+
+harmonic {
+    colvars         translation
+    centers         0.0
+    forceConstant   4184
+}
+
+colvar {
+    name orientation
+    orientation {
+        atoms {
+            indexGroup $protein_selection
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+harmonic {
+    colvars         orientation
+    centers         (1.0, 0.0, 0.0, 0.0)
+    forceConstant   836.8
+}

BFEE2/templates_gromacs/001.generate_tpr_sh.template

@@ -0,0 +1,31 @@
+#!/bin/sh
+
+# define the binary of gromacs
+if which gmx_mpi &> /dev/null; then
+    GMX_BIN=$(which gmx_mpi)
+else which gmx &> /dev/null;
+    GMX_BIN=$(which gmx)
+fi
+echo "Will use the gromacs executable binary at $GMX_BIN"
+
+# input (.gro, .top and .mdp) and output (.tpr)
+# MDP_FILE: running parameters
+# GRO_FILE: atom positions
+# TOP_FILE: topology
+MDP_FILE=$MDP_FILE_TEMPLATE
+GRO_FILE=$GRO_FILE_TEMPLATE
+TOP_FILE=$TOP_FILE_TEMPLATE
+
+# generate the tpr file
+OUTPUT_BASENAME=$(basename "$(pwd)")
+TPR_FILE="$OUTPUT_BASENAME.tpr"
+NEW_MDP_FILE="$OUTPUT_BASENAME.mdp"
+echo "Making gromacs tpr file ($TPR_FILE)..."
+$GMX_BIN grompp -f $MDP_FILE -c $GRO_FILE -p $TOP_FILE -o $TPR_FILE -po $NEW_MDP_FILE
+
+# run the PMF calculation
+mkdir -p output
+DEFAULT_OUTPUT_FILENAME="output/$OUTPUT_BASENAME.out"
+# $GMX_BIN mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s $TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME -colvars colvar.dat
+echo "You can now run gromacs by the following example:"
+echo "$GMX_BIN mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s $TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME -colvars $COLVARS_INPUT_TEMPLATE"

BFEE2/templates_gromacs/001.mdp.template

@@ -0,0 +1,70 @@
+;equilibration of p41-abl
+
+;Run control
+integrator          = md
+dt                  = $dt
+tinit               = 0
+nsteps              = $nsteps
+comm-mode           = Linear
+nstcomm             = 1000
+
+;Langevin dynamics
+bd-fric             = 0
+ld-seed             = -1
+
+;Energy minimization
+;emtol               = 10
+;emstep              = 0.01
+
+;Output control
+nstxout             = 5000
+nstvout             = 5000
+nstfout             = 5000
+nstlog              = 5000
+nstcalcenergy       = 1000
+nstenergy           = 5000
+
+;Neighbor searching
+cutoff-scheme       = Verlet
+ns-type             = grid
+pbc                 = xyz
+periodic-molecules  = no
+
+;Electrostatics
+coulombtype         = PME
+coulomb-modifier    = Potential-shift-Verlet
+rcoulomb            = 1.2
+
+;VdW
+vdwtype             = Cut-off
+vdw-modifier        = force-switch
+rvdw                = 1.2
+rvdw-switch         = 1.0
+DispCorr            = no
+
+;Bonds (for minimization)
+constraint-algorithm    = LINCS
+constraints             = h-bonds
+continuation            = yes
+morse                   = no
+
+;Implicit solvent
+implicit-solvent    = no
+
+;Pressure coupling
+;Pressure coupling
+pcoupl              = C-rescale
+pcoupltype          = Isotropic
+nstpcouple          = -1
+tau-p               = 2
+compressibility     = 4.5e-5
+ref-p               = $pressure
+
+;Temperature coupling
+tcoupl              = v-rescale
+tc-grps             = System
+tau_t               = 0.1
+ref_t               = $temperature
+
+;Velocity generation
+gen-vel             = no

BFEE2/templates_gromacs/001.readme.template

@@ -0,0 +1 @@
+ 

BFEE2/templates_gromacs/002.colvars.template

@@ -0,0 +1,101 @@
+colvarsTrajFrequency    500
+colvarsRestartFrequency 50000
+indexFile               colvars.ndx
+
+colvar {
+    name RMSD
+    rmsd {
+        atoms {
+            indexGroup $ligand_selection
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+colvar {
+    name                    eulerTheta
+    width                   $eulerTheta_width
+    lowerboundary           $eulerTheta_lower_boundary
+    upperboundary           $eulerTheta_upper_boundary
+    subtractAppliedForce    on
+    extendedLagrangian      on
+    extendedFluctuation     $eulerTheta_width
+    eulerTheta {
+        atoms {
+            indexGroup          $ligand_selection
+            centerToReference   on
+            rotateToReference   on
+            centerToOrigin      on
+            enableFitGradients  on
+            fittingGroup {
+                indexGroup $protein_selection
+            }
+            refPositionsfile reference.xyz
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+
+harmonicWalls {
+    colvars             eulerTheta
+    lowerWalls          $eulerTheta_lower_boundary
+    upperWalls          $eulerTheta_upper_boundary
+    lowerWallConstant   $eulerTheta_wall_constant
+    upperWallConstant   $eulerTheta_wall_constant
+}
+
+
+abf {
+    colvars             eulerTheta
+    FullSamples         10000
+    historyfreq         50000
+    writeCZARwindowFile
+}
+metadynamics {
+    colvars             eulerTheta
+    hillWidth           3.0
+    hillWeight          0.2092
+    wellTempered        on
+    biasTemperature     4000
+}
+
+harmonic {
+    colvars         RMSD
+    forceConstant   4184
+    centers         0
+}
+
+colvar {
+    name translation
+    distance {
+        group1 {
+            indexGroup $protein_selection
+        }
+        group2 {
+            dummyAtom $protein_center
+        }
+    }
+}
+
+harmonic { 
+    colvars         translation 
+    centers         0.0 
+    forceConstant   4184
+}
+
+colvar {
+    name orientation
+    orientation {
+        atoms {
+            indexGroup $protein_selection
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+harmonic { 
+    colvars         orientation
+    centers         (1.0, 0.0, 0.0, 0.0)
+    forceConstant   836.8
+}

BFEE2/templates_gromacs/002.generate_tpr_sh.template

@@ -0,0 +1,31 @@
+#!/bin/sh
+
+# define the binary of gromacs
+if which gmx_mpi &> /dev/null; then
+    GMX_BIN=$(which gmx_mpi)
+else which gmx &> /dev/null;
+    GMX_BIN=$(which gmx)
+fi
+echo "Will use the gromacs executable binary at $GMX_BIN"
+
+# input (.gro, .top and .mdp) and output (.tpr)
+# MDP_FILE: running parameters
+# GRO_FILE: atom positions
+# TOP_FILE: topology
+MDP_FILE=$MDP_FILE_TEMPLATE
+GRO_FILE=$GRO_FILE_TEMPLATE
+TOP_FILE=$TOP_FILE_TEMPLATE
+
+# generate the tpr file
+OUTPUT_BASENAME=$(basename "$(pwd)")
+TPR_FILE="$OUTPUT_BASENAME.tpr"
+NEW_MDP_FILE="$OUTPUT_BASENAME.mdp"
+echo "Making gromacs tpr file ($TPR_FILE)..."
+$GMX_BIN grompp -f $MDP_FILE -c $GRO_FILE -p $TOP_FILE -o $TPR_FILE -po $NEW_MDP_FILE
+
+# run the PMF calculation
+mkdir -p output
+DEFAULT_OUTPUT_FILENAME="output/$OUTPUT_BASENAME.out"
+# $GMX_BIN mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s $TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME -colvars colvar.dat
+echo "You can now run gromacs by the following example:"
+echo "$GMX_BIN mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s $TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME -colvars $COLVARS_INPUT_TEMPLATE"

BFEE2/templates_gromacs/002.mdp.template

@@ -0,0 +1,70 @@
+;equilibration of p41-abl
+
+;Run control
+integrator          = md
+dt                  = $dt
+tinit               = 0
+nsteps              = $nsteps
+comm-mode           = Linear
+nstcomm             = 1000
+
+;Langevin dynamics
+bd-fric             = 0
+ld-seed             = -1
+
+;Energy minimization
+;emtol               = 10
+;emstep              = 0.01
+
+;Output control
+nstxout             = 5000
+nstvout             = 5000
+nstfout             = 5000
+nstlog              = 5000
+nstcalcenergy       = 1000
+nstenergy           = 5000
+
+;Neighbor searching
+cutoff-scheme       = Verlet
+ns-type             = grid
+pbc                 = xyz
+periodic-molecules  = no
+
+;Electrostatics
+coulombtype         = PME
+coulomb-modifier    = Potential-shift-Verlet
+rcoulomb            = 1.2
+
+;VdW
+vdwtype             = Cut-off
+vdw-modifier        = force-switch
+rvdw                = 1.2
+rvdw-switch         = 1.0
+DispCorr            = no
+
+;Bonds (for minimization)
+constraint-algorithm    = LINCS
+constraints             = h-bonds
+continuation            = yes
+morse                   = no
+
+;Implicit solvent
+implicit-solvent    = no
+
+;Pressure coupling
+;Pressure coupling
+pcoupl              = C-rescale
+pcoupltype          = Isotropic
+nstpcouple          = -1
+tau-p               = 2
+compressibility     = 4.5e-5
+ref-p               = $pressure
+
+;Temperature coupling
+tcoupl              = v-rescale
+tc-grps             = System
+tau_t               = 0.1
+ref_t               = $temperature
+
+;Velocity generation
+gen-vel             = no

BFEE2/templates_gromacs/003.colvars.template

@@ -0,0 +1,125 @@
+colvarsTrajFrequency    500
+colvarsRestartFrequency 50000
+indexFile               colvars.ndx
+
+colvar {
+    name RMSD
+    rmsd {
+        atoms {
+            indexGroup $ligand_selection
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+colvar {
+    name                eulerTheta
+    eulerTheta {
+        atoms {
+            indexGroup          $ligand_selection
+            centerToReference   on
+            rotateToReference   on
+            centerToOrigin      on
+            enableFitGradients  on
+            fittingGroup {
+                indexGroup $protein_selection
+            }
+            refPositionsfile reference.xyz
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+colvar {
+    name                    eulerPhi
+    width                   $eulerPhi_width 
+    lowerboundary           $eulerPhi_lower_boundary 
+    upperboundary           $eulerPhi_upper_boundary
+    subtractAppliedForce    on
+    extendedLagrangian      on
+    extendedFluctuation     $eulerPhi_width
+    eulerPhi {
+        atoms {
+            indexGroup          $ligand_selection
+            centerToReference   on
+            rotateToReference   on
+            centerToOrigin      on
+            enableFitGradients  on
+            fittingGroup {
+                indexGroup $protein_selection
+            }
+            refPositionsfile reference.xyz
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+harmonicWalls {
+    colvars             eulerPhi
+    lowerWalls          $eulerPhi_lower_boundary
+    upperWalls          $eulerPhi_upper_boundary
+    lowerWallConstant   $eulerPhi_wall_constant
+    upperWallConstant   $eulerPhi_wall_constant
+}
+
+abf {
+    colvars             eulerPhi
+    FullSamples         10000
+    historyfreq         50000
+    writeCZARwindowFile
+}
+
+metadynamics {
+    colvars             eulerPhi
+    hillWidth           3.0
+    hillWeight          0.2092
+    wellTempered        on
+    biasTemperature     4000
+}
+
+harmonic {
+   colvars          eulerTheta
+   forceConstant    0.4184
+   centers          002_pmf_argmin
+}
+
+
+harmonic {
+   colvars          RMSD
+   forceConstant    4184
+   centers          0
+}
+
+colvar {
+    name translation
+    distance {
+        group1 {
+            indexGroup $protein_selection
+        }
+        group2 {
+            dummyAtom $protein_center
+        }
+    }
+}
+
+harmonic { 
+    colvars         translation 
+    centers         0.0 
+    forceConstant   4184 
+}
+
+colvar {
+    name orientation
+    orientation {
+        atoms {
+            indexGroup $protein_selection
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+harmonic { 
+    colvars         orientation
+    centers         (1.0, 0.0, 0.0, 0.0)
+    forceConstant   836.8
+}

BFEE2/templates_gromacs/003.generate_tpr_sh.template

@@ -0,0 +1,36 @@
+#!/bin/sh
+
+# define the binary of gromacs
+if which gmx_mpi &> /dev/null; then
+    GMX_BIN=$(which gmx_mpi)
+else which gmx &> /dev/null;
+    GMX_BIN=$(which gmx)
+fi
+echo "Will use the gromacs executable binary at $GMX_BIN"
+
+# input (.gro, .top and .mdp) and output (.tpr)
+# MDP_FILE: running parameters
+# GRO_FILE: atom positions
+# TOP_FILE: topology
+MDP_FILE=$MDP_FILE_TEMPLATE
+GRO_FILE=$GRO_FILE_TEMPLATE
+TOP_FILE=$TOP_FILE_TEMPLATE
+
+# generate the tpr file
+OUTPUT_BASENAME=$(basename "$(pwd)")
+TPR_FILE="$OUTPUT_BASENAME.tpr"
+NEW_MDP_FILE="$OUTPUT_BASENAME.mdp"
+echo "Making gromacs tpr file ($TPR_FILE)..."
+$GMX_BIN grompp -f $MDP_FILE -c $GRO_FILE -p $TOP_FILE -o $TPR_FILE -po $NEW_MDP_FILE
+
+# modify the colvars input file using the PMF minima in previous stages
+ARGMIN_002=$(awk -f ./find_min_max.awk ../$BASENAME_002/output/$BASENAME_002.out.abf1.czar.pmf)
+sed -i.orig "s/002_pmf_argmin/$ARGMIN_002/g" $COLVARS_INPUT_TEMPLATE
+rm -f $COLVARS_INPUT_TEMPLATE.orig
+
+# run the PMF calculation
+mkdir -p output
+DEFAULT_OUTPUT_FILENAME="output/$OUTPUT_BASENAME.out"
+# $GMX_BIN mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s $TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME -colvars colvar.dat
+echo "You can now run gromacs by the following example:"
+echo "$GMX_BIN mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s $TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME -colvars $COLVARS_INPUT_TEMPLATE"

BFEE2/templates_gromacs/003.mdp.template

@@ -0,0 +1,70 @@
+;equilibration of p41-abl
+
+;Run control
+integrator          = md
+dt                  = $dt
+tinit               = 0
+nsteps              = $nsteps
+comm-mode           = Linear
+nstcomm             = 1000
+
+;Langevin dynamics
+bd-fric             = 0
+ld-seed             = -1
+
+;Energy minimization
+;emtol               = 10
+;emstep              = 0.01
+
+;Output control
+nstxout             = 5000
+nstvout             = 5000
+nstfout             = 5000
+nstlog              = 5000
+nstcalcenergy       = 1000
+nstenergy           = 5000
+
+;Neighbor searching
+cutoff-scheme       = Verlet
+ns-type             = grid
+pbc                 = xyz
+periodic-molecules  = no
+
+;Electrostatics
+coulombtype         = PME
+coulomb-modifier    = Potential-shift-Verlet
+rcoulomb            = 1.2
+
+;VdW
+vdwtype             = Cut-off
+vdw-modifier        = force-switch
+rvdw                = 1.2
+rvdw-switch         = 1.0
+DispCorr            = no
+
+;Bonds (for minimization)
+constraint-algorithm    = LINCS
+constraints             = h-bonds
+continuation            = yes
+morse                   = no
+
+;Implicit solvent
+implicit-solvent    = no
+
+;Pressure coupling
+;Pressure coupling
+pcoupl              = C-rescale
+pcoupltype          = Isotropic
+nstpcouple          = -1
+tau-p               = 2
+compressibility     = 4.5e-5
+ref-p               = $pressure
+
+;Temperature coupling
+tcoupl              = v-rescale
+tc-grps             = System
+tau_t               = 0.1
+ref_t               = $temperature
+
+;Velocity generation
+gen-vel             = no