bfee2 3.1.1.post1__py3-none-any.whl

BFEE2/templates_gromacs/007_eq.colvars.template

@@ -0,0 +1,169 @@
+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
+    eulerPhi {
+        atoms {
+            indexGroup          $ligand_selection
+            centerToReference   on
+            rotateToReference   on
+            centerToOrigin      on
+            enableFitGradients  on
+            fittingGroup {
+                indexGroup $protein_selection
+            }
+            refPositionsfile reference.xyz
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+colvar {
+    name                eulerPsi
+    eulerPsi {
+        atoms {
+            indexGroup          $ligand_selection
+            centerToReference   on
+            rotateToReference   on
+            centerToOrigin      on
+            enableFitGradients  on
+            fittingGroup {
+                indexGroup $protein_selection
+            }
+            refPositionsfile reference.xyz
+        }
+        refPositionsfile reference.xyz
+    }
+}
+
+colvar {
+    name polarTheta
+    polarTheta {
+        atoms {
+            indexGroup        $ligand_selection
+            centerToReference on
+            rotateToReference on
+            centerToOrigin    on
+            fittingGroup {
+                indexGroup $protein_selection
+            }
+            refPositionsfile reference.xyz
+        }
+    }
+}
+
+colvar {
+    name                    polarPhi
+    polarPhi {
+        atoms {
+            indexGroup        $ligand_selection
+            centerToReference on
+            rotateToReference on
+            centerToOrigin    on
+            fittingGroup {
+                indexGroup  $protein_selection
+            }
+            refPositionsFile reference.xyz
+        }
+    }
+}
+
+harmonic {
+    colvars             polarPhi
+    forceConstant       0.4184
+    centers             006_pmf_argmin
+}
+
+harmonic {
+    colvars             polarTheta
+    forceConstant       0.4184
+    centers             005_pmf_argmin
+}
+
+harmonic {
+    colvars             eulerPsi
+    forceConstant       0.4184
+    centers             004_pmf_argmin
+}
+
+harmonic {
+    colvars             eulerPhi
+    forceConstant       0.4184
+    centers             003_pmf_argmin
+}
+
+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/007_eq.generate_tpr_sh.template

@@ -0,0 +1,64 @@
+#!/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
+
+# enlarge the pbc box
+echo "Enlarge the box to $NEW_BOX_X_TEMPLATE $NEW_BOX_Y_TEMPLATE $NEW_BOX_Z_TEMPLATE"
+$GMX_BIN editconf -f $GRO_FILE -box $NEW_BOX_X_TEMPLATE $NEW_BOX_Y_TEMPLATE $NEW_BOX_Z_TEMPLATE -o $BOX_MODIFIED_GRO_TEMPLATE
+# add more solvents to the new box
+NEW_TOP_FILE=$MODIFIED_TOP_TEMPLATE
+NEW_GRO_FILE=$MODIFIED_GRO_TEMPLATE
+cp -f $TOP_FILE $NEW_TOP_FILE
+echo "Add more solvent molecules to fill the box..."
+$GMX_BIN solvate -cp $BOX_MODIFIED_GRO_TEMPLATE -cs solvent.gro -p $NEW_TOP_FILE -box $NEW_BOX_X_TEMPLATE $NEW_BOX_Y_TEMPLATE $NEW_BOX_Z_TEMPLATE -o $NEW_GRO_FILE
+
+# generate the tpr file for minimization
+OUTPUT_BASENAME=$(basename "$(pwd)")
+MIN_MDP_FILE=$MIN_MDP_FILE_TEMPLATE
+MIN_TPR_FILE="$OUTPUT_BASENAME.min.tpr"
+NEW_MIN_MDP_FILE="$OUTPUT_BASENAME.min.new.mdp"
+echo "Making gromacs tpr file ($MIN_TPR_FILE) for minimization..."
+$GMX_BIN grompp -f $MIN_MDP_FILE -c $NEW_GRO_FILE -p $NEW_TOP_FILE -o $MIN_TPR_FILE -po $NEW_MIN_MDP_FILE
+
+# run minimization
+mkdir -p output_minimization
+DEFAULT_OUTPUT_FILENAME="output_minimization/$OUTPUT_BASENAME.min.out"
+$GMX_BIN mdrun -s $MIN_TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME
+
+# generate the tpr file
+OUTPUT_BASENAME=$(basename "$(pwd)")
+TPR_FILE="$OUTPUT_BASENAME.eq.tpr"
+NEW_MDP_FILE="$OUTPUT_BASENAME.mdp"
+NEW_GRO_FILE="$DEFAULT_OUTPUT_FILENAME.gro"
+echo "Making gromacs tpr file ($TPR_FILE)..."
+$GMX_BIN grompp -f $MDP_FILE -c $NEW_GRO_FILE -p $NEW_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)
+ARGMIN_003=$(awk -f ./find_min_max.awk ../$BASENAME_003/output/$BASENAME_003.out.abf1.czar.pmf)
+ARGMIN_004=$(awk -f ./find_min_max.awk ../$BASENAME_004/output/$BASENAME_004.out.abf1.czar.pmf)
+ARGMIN_005=$(awk -f ./find_min_max.awk ../$BASENAME_005/output/$BASENAME_005.out.abf1.czar.pmf)
+ARGMIN_006=$(awk -f ./find_min_max.awk ../$BASENAME_006/output/$BASENAME_006.out.abf1.czar.pmf)
+sed -i.orig "s/002_pmf_argmin/$ARGMIN_002/g; s/003_pmf_argmin/$ARGMIN_003/g; s/004_pmf_argmin/$ARGMIN_004/g; s/005_pmf_argmin/$ARGMIN_005/g; s/006_pmf_argmin/$ARGMIN_006/g" $COLVARS_INPUT_TEMPLATE
+rm -f $COLVARS_INPUT_TEMPLATE.orig
+
+# run the PMF calculation
+mkdir -p output
+DEFAULT_OUTPUT_FILENAME="output/${OUTPUT_BASENAME}_eq.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"

BFEE2/templates_gromacs/007_min.mdp.template

@@ -0,0 +1,62 @@
+;minimization
+
+;Run control
+integrator          = steep
+dt                  = $dt
+tinit               = 0
+nsteps              = $nsteps
+comm-mode           = Linear
+nstcomm             = 10
+
+;Langevin dynamics
+bd-fric             = 0
+ld-seed             = -1
+
+;Energy minimization
+emtol               = 10
+emstep              = 0.01
+
+;Output control
+nstxout             = 100
+nstvout             = 100
+nstfout             = 100
+nstlog              = 100
+nstcalcenergy       = 10
+nstenergy           = 100 
+
+;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             = none
+continuation            = no
+morse                   = no
+
+;Implicit solvent
+implicit-solvent    = no
+
+;Pressure coupling
+pcoupl              = no
+
+;Velocity generation
+gen-vel             = yes
+
+;Colvars
+;colvars-active = no
+;colvars-configfile = $colvarsFile

BFEE2/templates_gromacs/008.colvars.template

@@ -0,0 +1,42 @@
+colvarsTrajFrequency    500
+colvarsRestartFrequency 50000
+indexFile               colvars_ligand_only.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_ligand_only.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
+}
+
+metadynamics {
+    colvars             RMSD
+    hillWidth           3.0
+    hillWeight          0.2092
+    wellTempered        on
+    biasTemperature     4000
+}

BFEE2/templates_gromacs/008.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"

BFEE2/templates_gromacs/008.mdp.template

@@ -0,0 +1,74 @@
+;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
+
+;Colvars
+colvars-active = yes
+colvars-configfile = $colvarsFile

BFEE2/templates_gromacs/008_eq.colvars.template

@@ -0,0 +1,14 @@
+colvarsTrajFrequency    500
+colvarsRestartFrequency 50000
+indexFile               colvars_ligand_only.ndx
+
+colvar {
+    name                    RMSD
+    rmsd {
+        atoms {
+            indexGroup $ligand_selection
+        }
+        refPositionsfile reference_ligand_only.xyz
+    }
+}
+

BFEE2/templates_gromacs/008_eq.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="$OUTPUT_BASENAME.eq.tpr"
+NEW_MDP_FILE="$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}_eq.out"
+# $GMX_BIN mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s $TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME
+echo "You can now run gromacs by the following example:"
+echo "$GMX_BIN mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s $TPR_FILE -deffnm $DEFAULT_OUTPUT_FILENAME"