diff --git a/EAPM/EAPM.py b/EAPM/EAPM.py
index a7ad8f3..d6f6c1c 100644
--- a/EAPM/EAPM.py
+++ b/EAPM/EAPM.py
@@ -95,13 +95,21 @@ def createPlugin():
 
     eapmPlugin.addBlock(epPredBlock)
 
-    from Blocks.testBlock import testBlock  # type: ignore
+    # from Blocks.testBlock import testBlock  # type: ignore
 
-    eapmPlugin.addBlock(testBlock)
+    # eapmPlugin.addBlock(testBlock)
 
-    from Blocks.AnalyseGlideGPX import AnalyseGPXBlock  # type: ignore
+    from Blocks.AnalyseGlide import AnalyseGBlock  # type: ignore
 
-    eapmPlugin.addBlock(AnalyseGPXBlock)
+    eapmPlugin.addBlock(AnalyseGBlock)
+
+    # from Blocks.Rbcavity import rbCavityBlock  # type: ignore
+
+    # eapmPlugin.addBlock(rbCavityBlock)
+
+    # from Blocks.Rbdock import rbDockBlock  # type: ignore
+
+    # eapmPlugin.addBlock(rbDockBlock)
 
     # Add the configs
     from Configs.mafftConfig import mafftExecutableConfig  # type: ignore
diff --git a/EAPM/Include/Blocks/Ahatool.py b/EAPM/Include/Blocks/Ahatool.py
index 1e6e64b..e1865e3 100644
--- a/EAPM/Include/Blocks/Ahatool.py
+++ b/EAPM/Include/Blocks/Ahatool.py
@@ -1,7 +1,3 @@
-import datetime
-import os
-import subprocess
-
 from HorusAPI import PluginBlock, PluginVariable, VariableList, VariableTypes
 
 # TODO Add to the documentation
@@ -85,6 +81,10 @@
 
 def initialAction(block: PluginBlock):
 
+    import datetime
+    import os
+    import subprocess
+
     container_name = block.inputs.get("container_name", "bsceapm/ahatool:2.2")
     input_fasta = block.inputs.get("input_fasta", None)
     fasta = os.path.basename(input_fasta)
diff --git a/EAPM/Include/Blocks/AlignPdbEAPM.py b/EAPM/Include/Blocks/AlignPdbEAPM.py
index 5593445..d3ef54a 100644
--- a/EAPM/Include/Blocks/AlignPdbEAPM.py
+++ b/EAPM/Include/Blocks/AlignPdbEAPM.py
@@ -124,26 +124,30 @@ def initialAlign(block: PluginBlock):
     alignmentMode = block.variables.get("alignment_mode", "aligned")
     referenceResidues = block.variables.get("reference_residues", [])
 
+    import prepare_proteins
+
+    print("Loading PDB files...")
+
+    models = prepare_proteins.proteinModels(inputFolder)
+
     # Parse the chain indexes
     if chainIndexes is not None:
         chainIndexes = [x["chain_index"] for x in chainIndexes]
     else:
         chainIndexes = [0]
 
+    trajectory_chain_indexes = None
     # Parse the trajectory chain indexes
     if trajectoryChainIndexes is not None:
         trajectoryChainIndexes = [x["trajectory_chain_index"] for x in trajectoryChainIndexes]
+        trajectory_chain_indexes = {}
+        for i, model in enumerate(models.models_names):
+            trajectory_chain_indexes[model] = trajectoryChainIndexes[i]
 
     # Parse the reference residues
     if referenceResidues is not None:
         referenceResidues = [x["reference_residues"] for x in referenceResidues]
 
-    import prepare_proteins
-
-    print("Loading PDB files...")
-
-    models = prepare_proteins.proteinModels(inputFolder)
-
     print("Aligning models...")
 
     import subprocess
@@ -163,7 +167,7 @@ def hookSubprocessMafft(command, **kwargs):
             pdbReference,
             outputFolder,
             chain_indexes=chainIndexes,
-            trajectory_chain_indexes=trajectoryChainIndexes,
+            trajectory_chain_indexes=trajectory_chain_indexes,
             aligment_mode=alignmentMode,
             reference_residues=referenceResidues,
             verbose=True,
diff --git a/EAPM/Include/Blocks/AlphaFoldEAPM.py b/EAPM/Include/Blocks/AlphaFoldEAPM.py
index 815c9d8..9c80b10 100644
--- a/EAPM/Include/Blocks/AlphaFoldEAPM.py
+++ b/EAPM/Include/Blocks/AlphaFoldEAPM.py
@@ -2,8 +2,6 @@
 Module containing the AlphaFold block for the EAPM plugin
 """
 
-import os
-
 from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # ==========================#
@@ -72,6 +70,8 @@ def initialAlphafold(block: SlurmBlock):
         print("Alphafold requires an accelerated partition. Changing to acc_bscls.")
         block.variables["partition"] = "acc_bscls"
 
+    import os
+
     # If folder already exists, raise exception
     if removeExisting and os.path.exists(folderName):
         os.system("rm -rf " + folderName)
@@ -107,6 +107,8 @@ def finalAlhafoldAction(block: SlurmBlock):
 
     resultsFolder = block.extraData["folder_name"]
 
+    import os
+
     output_models_folder = os.path.join(downloaded_path, resultsFolder, "output_models")
 
     block.setOutput(outputModelsVariable.id, output_models_folder)
diff --git a/EAPM/Include/Blocks/AnalyseGlideGPX.py b/EAPM/Include/Blocks/AnalyseGlide.py
similarity index 55%
rename from EAPM/Include/Blocks/AnalyseGlideGPX.py
rename to EAPM/Include/Blocks/AnalyseGlide.py
index 425a48a..cd3c048 100644
--- a/EAPM/Include/Blocks/AnalyseGlideGPX.py
+++ b/EAPM/Include/Blocks/AnalyseGlide.py
@@ -1,11 +1,3 @@
-import json
-import os
-import shutil
-
-import bsc_calculations
-import pandas as pd
-import prepare_proteins
-
 from HorusAPI import PluginBlock, PluginVariable, VariableGroup, VariableTypes
 
 # TODO  Configure the inputs correctly
@@ -28,10 +20,16 @@
     defaultValue=None,
 )
 residueProtein = PluginVariable(
-    name="Atom Protein", id="resi_id1", description="atom1", type=VariableTypes.ATOM
+    name="Atom Protein",
+    id="resi_id1",
+    description="Atom of the protein to calculate the distance to",
+    type=VariableTypes.ATOM,
 )
 residueLigand = PluginVariable(
-    name="Atom Ligand", id="resi_id2", description="atom2", type=VariableTypes.ATOM
+    name="Atom Ligand",
+    id="resi_id2",
+    description="Atom of the ligand to calculate the distance to",
+    type=VariableTypes.ATOM,
 )
 resNameProt = PluginVariable(
     name="Protein residue name",
@@ -40,10 +38,10 @@
     type=VariableTypes.STRING,
     defaultValue="CYS",
 )
-resNameLig = PluginVariable(
-    name="Ligand residue name",
-    id="res_name_lig",
-    description="The ligand residue name",
+atomNameProt = PluginVariable(
+    name="Protein atomname",
+    id="atom_name_prot",
+    description="The protein atom name",
     type=VariableTypes.STRING,
     defaultValue="SG",
 )
@@ -54,12 +52,26 @@
     type=VariableTypes.STRING,
     defaultValue="GSH",
 )
+atomNameLig = PluginVariable(
+    name="Ligand atom name",
+    id="atom_name_ligand",
+    description="The atom name of the ligand",
+    type=VariableTypes.STRING,
+    defaultValue="S1",
+)
 
 stringGroup = VariableGroup(
     id="string_input",
     name="Input String",
     description="The input are in string",
-    variables=[conservedResidues, glideOutputVariable, resNameProt, resNameLig, ligandName],
+    variables=[
+        conservedResidues,
+        glideOutputVariable,
+        resNameProt,
+        atomNameProt,
+        ligandName,
+        atomNameLig,
+    ],
 )
 atomGroup = VariableGroup(
     id="atom_input",
@@ -70,12 +82,18 @@
 
 # Output variables
 outputModelsVariable = PluginVariable(
-    id="models",
-    name="Alphafold models",
-    description="The output models",
+    id="best_poses",
+    name="Best poses",
+    description="The best poses from the analysis",
     type=VariableTypes.FOLDER,
 )
-
+analyseGlideOutputVariable = PluginVariable(
+    id="glide_results_output",
+    name="Glide results output",
+    description="Output results of the Glide analysis",
+    type=VariableTypes.CUSTOM,
+    allowedValues=["glide_output"],
+)
 
 # ==========================#
 # Variable
@@ -87,10 +105,26 @@
     type=VariableTypes.STRING,
     defaultValue="SG_S",
 )
+removePreviousVar = PluginVariable(
+    name="Remove previous models",
+    id="remove_previous",
+    description="Remove previous",
+    type=VariableTypes.BOOLEAN,
+    defaultValue=False,
+)
+separatorVar = PluginVariable(
+    name="Separator",
+    id="separator",
+    description="The separator",
+    type=VariableTypes.STRING,
+    defaultValue="@",
+)
 
 
 def finalAction(block: PluginBlock):
 
+    import prepare_proteins
+
     bsc_result = block.inputs.get(glideOutputVariable.id, None)
     folder_to_analyse = bsc_result["dock_folder"]
     model_folder = bsc_result["model_folder"]
@@ -98,43 +132,58 @@ def finalAction(block: PluginBlock):
     conserved_indexes = block.inputs.get(conservedResidues.id, None)
 
     metrics = block.variables.get("metrics", "SG_S")
+    remove_previous = block.variables.get("remove_previous", False)
+    separator = block.variables.get("separator", "@")
 
     if block.selectedInputGroup == stringGroup.id:
         res_name_prot = block.inputs.get(resNameProt.id, "CYS")
-        res_name_lig = block.inputs.get(resNameLig.id, "SG")
+        atom_name_prot = block.inputs.get(atomNameProt.id, "SG")
         ligand_name = block.inputs.get(ligandName.id, "GSH")
+        atom_name_lig = block.inputs.get(atomNameLig.id, "S1")
     else:
         residue_protein = block.inputs.get(residueProtein.id, None)
+        res_name_prot = residue_protein["auth_comp_id"]
+        atom_name_prot = residue_protein["auth_atom_id"]
         residue_ligand = block.inputs.get(residueLigand.id, None)
+        ligand_name = residue_ligand["auth_comp_id"]
+        atom_name_lig = residue_ligand["auth_atom_id"]
+        metrics = f"{atom_name_prot}_{atom_name_lig}"
 
     models = prepare_proteins.proteinModels(model_folder)
 
+    if conserved_indexes is None:
+        raise ValueError("Conserved residues must be provided")
+    if not isinstance(conserved_indexes, dict):
+        try:
+            conserved_indexes = int(conserved_indexes)
+        except ValueError:
+            raise ValueError("Conserved indexes must be an integer or a dictionary of integers")
+        conserved_indexes_f = {}
+        for model in models:
+            conserved_indexes_f[model] = [conserved_indexes]
+        conserved_indexes = conserved_indexes_f
+
     center_atom = {}  # Create dictionary to store the atom 3-element tuple for each model
     for model in models:  # Iterate the models inside the library
         # Iterate the residues for each Bio.PDB.Structure object
         for r in models.structures[model].get_residues():
             # Check that the residue matches the defined index
-            aa = conserved_indexes[model]
             # for cons_ind in conserved_indexes[model]:
             if r.id[1] in conserved_indexes[model]:
                 # Assert that the residue has the correct residue identity
                 if r.resname == res_name_prot:
                     # Store the corresponsing tuple.
-                    center_atom[model] = (r.get_parent().id, r.id[1], res_name_lig)
+                    center_atom[model] = (r.get_parent().id, r.id[1], atom_name_prot)
                     break
 
-    print(f"center_atom: {center_atom}")
-
     atom_pairs = {}  # Define the dictionary containing the atom pairs for each model
     for model in models:
         atom_pairs[model] = {}
         for ligand in [ligand_name]:
             atom_pairs[model][ligand] = []
-            atom_pairs[model][ligand].append((center_atom[model], "S1"))
+            atom_pairs[model][ligand].append((center_atom[model], atom_name_lig))
 
-    print(f"Atom pairs: {atom_pairs}")
-
-    models.analyseDocking(folder_to_analyse, atom_pairs=atom_pairs)
+    models.analyseDocking(folder_to_analyse, atom_pairs=atom_pairs, separator=separator)
 
     metric_distances = {}  # Define the global dictionary
     metric_distances[metrics] = {}  # Define the metric nested dictionary
@@ -144,24 +193,38 @@ def finalAction(block: PluginBlock):
             # Define the ligand nested dictionary with all the docking distances list
             metric_distances[metrics][model][ligand] = models.getDockingDistances(model, ligand)
 
-    print(f"metric_distances: {metric_distances}")
-
     models.combineDockingDistancesIntoMetrics(metric_distances)
 
-    print(f"models.docking_data: {models.docking_data}")
-
     best_poses = models.getBestDockingPosesIteratively(metric_distances)
 
-    models.extractDockingPoses(best_poses, folder_to_analyse, "best_docking_poses", separator="@")
+    models.extractDockingPoses(
+        best_poses,
+        folder_to_analyse,
+        "best_docking_poses",
+        separator=separator,
+        remove_previous=remove_previous,
+    )
 
     block.setOutput(outputModelsVariable.id, "best_docking_poses")
 
+    glideOutput = {
+        "poses_folder": "best_docking_poses",
+        "models_folder": model_folder,  # "prepared_proteins",
+        "atom_pairs": atom_pairs,
+    }
+    import pickle
+
+    with open("glide_output.pkl", "wb") as f:
+        pickle.dump(glideOutput, f)
+
+    block.setOutput(analyseGlideOutputVariable.id, glideOutput)
+
 
-AnalyseGPXBlock = PluginBlock(
-    name="Analyse Glide GPX",
-    description="To analyse Glide GPX results",
+AnalyseGBlock = PluginBlock(
+    name="Analyse Glide",
+    description="To analyse Glide results",
     action=finalAction,
-    variables=[metricsVar],
-    inputGroups=[stringGroup, atomGroup],
-    outputs=[outputModelsVariable],
+    variables=[metricsVar, removePreviousVar, separatorVar],
+    inputGroups=[atomGroup, stringGroup],
+    outputs=[outputModelsVariable, analyseGlideOutputVariable],
 )
diff --git a/EAPM/Include/Blocks/AnalyseGlideDocking.py b/EAPM/Include/Blocks/AnalyseGlideDocking.py
index 504bc56..9d1056b 100644
--- a/EAPM/Include/Blocks/AnalyseGlideDocking.py
+++ b/EAPM/Include/Blocks/AnalyseGlideDocking.py
@@ -1,6 +1,3 @@
-import datetime
-import os
-
 from HorusAPI import (
     Extensions,
     PluginBlock,
@@ -133,6 +130,10 @@
 
 
 def analyseDockingAction(block: PluginBlock):
+
+    import datetime
+    import os
+
     if block.selectedInputGroup == "folder_variable_group":
         folder_to_analyse = block.inputs.get("docking_folder", "docking")
         model_folder = block.inputs.get("model_folder", "models")
@@ -391,6 +392,7 @@ def analyseDocking(
     """
 
     import json
+    import os
 
     import pandas as pd
     import prepare_proteins
@@ -529,6 +531,7 @@ def extractDockingPoses(
         Remove all content in the output folder
     """
 
+    import os
     import shutil
 
     # Check the separator is not in model or ligand names
diff --git a/EAPM/Include/Blocks/AsiteDesign.py b/EAPM/Include/Blocks/AsiteDesign.py
index 1bb9b39..3998ec2 100644
--- a/EAPM/Include/Blocks/AsiteDesign.py
+++ b/EAPM/Include/Blocks/AsiteDesign.py
@@ -2,10 +2,7 @@
 Module containing the Asitedesign block for the EAPM plugin
 """
 
-import os
-import subprocess
-
-from HorusAPI import PluginVariable, SlurmBlock, VariableList, VariableTypes
+from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # ==========================#
 # Variable inputs
@@ -72,6 +69,9 @@
 
 
 def initialAsite(block: SlurmBlock):
+    import os
+    import subprocess
+
     # Get the input variables
     input_yaml = block.inputs.get("input_yaml", None)
     input_params = block.inputs.get("input_params", None)
@@ -110,6 +110,9 @@ def initialAsite(block: SlurmBlock):
 
 
 def finalAsiteAction(block: SlurmBlock):
+
+    import os
+
     from utils import downloadResultsAction
 
     downloaded_path = downloadResultsAction(block)
diff --git a/EAPM/Include/Blocks/ConservedResiduesMSA.py b/EAPM/Include/Blocks/ConservedResiduesMSA.py
index bee7ae6..de12d8b 100644
--- a/EAPM/Include/Blocks/ConservedResiduesMSA.py
+++ b/EAPM/Include/Blocks/ConservedResiduesMSA.py
@@ -25,7 +25,7 @@
 
 
 def getConservedMSAPositions(block: PluginBlock):
-    proteinFolder = block.inputs.get("protein_folder", "proteins")
+    proteinFolder = block.inputs.get(proteinFolderVariable.id, "proteins")
 
     # Check that there is at least one pdb file in the folder
     import os
@@ -73,7 +73,7 @@ def hookSubprocessMafft(command, **kwargs):
         Extensions().loadHTML(html, title="Conserved residues")
 
         # Get the residue index to get
-        residueIndexes = block.variables.get("residue_index", [])
+        residueIndexes = block.variables.get(residueIndexToGetVariable.id, [])
 
         if residueIndexes is None or len(residueIndexes) == 0:
             # Get all the indexes
@@ -90,7 +90,7 @@ def hookSubprocessMafft(command, **kwargs):
             if len(conservedResidues[model]) == 0:
                 raise Exception(
                     "There are no conserved residues for the selected indexes: "
-                    + " ".join(residueIndexes)
+                    + " ".join(str(residueIndexes))
                 )
             break
 
diff --git a/EAPM/Include/Blocks/EpPred.py b/EAPM/Include/Blocks/EpPred.py
index 1d385a2..705d77b 100644
--- a/EAPM/Include/Blocks/EpPred.py
+++ b/EAPM/Include/Blocks/EpPred.py
@@ -1,8 +1,4 @@
-import datetime
-import os
-import subprocess
-
-from HorusAPI import PluginVariable, SlurmBlock, VariableList, VariableTypes
+from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # TODO Making the block to work in marenostrum, if not, will work in local.
 # TODO Add to documentation
@@ -199,6 +195,8 @@
 
 def runEppred(block: SlurmBlock):
 
+    import os
+
     inputfasta = block.inputs.get("input_fasta", None)
 
     if inputfasta is None:
diff --git a/EAPM/Include/Blocks/HmmAlign.py b/EAPM/Include/Blocks/HmmAlign.py
index d494eb1..b993faa 100644
--- a/EAPM/Include/Blocks/HmmAlign.py
+++ b/EAPM/Include/Blocks/HmmAlign.py
@@ -2,8 +2,6 @@
 Module containing the HmmAlign block for the EAPM plugin as a nord3 implementation
 """
 
-import os
-
 from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # ==========================#
@@ -52,6 +50,8 @@
 
 def runHmmAlign(block: SlurmBlock):
 
+    import os
+
     inputfasta = block.inputs.get("input_fasta", None)
     inputhmm = block.inputs.get("input_hmm", None)
 
@@ -88,7 +88,12 @@ def runHmmAlign(block: SlurmBlock):
     os.system(f"cp {inputfasta} {folderName}")
     os.system(f"cp {inputhmm} {folderName}")
 
-    jobs = [f"hmmalign {folderName}/{inputhmm} {folderName}/{inputfasta}"]
+    if block.remote.isLocal:
+        hmmerExecutable = block.config.get("hmmer_path", "hmmer") + "/hmmalign"
+    else:
+        hmmerExecutable = "hmmalign"
+
+    jobs = [f"{hmmerExecutable} {folderName}/{inputhmm} {folderName}/{inputfasta}"]
 
     from utils import launchCalculationAction
 
@@ -103,6 +108,8 @@ def runHmmAlign(block: SlurmBlock):
 
 
 def finalAction(block: SlurmBlock):
+    import os
+
     from utils import downloadResultsAction
 
     downloaded_path = downloadResultsAction(block)
diff --git a/EAPM/Include/Blocks/HmmBuild.py b/EAPM/Include/Blocks/HmmBuild.py
index 6d5a3cc..9f54e7c 100644
--- a/EAPM/Include/Blocks/HmmBuild.py
+++ b/EAPM/Include/Blocks/HmmBuild.py
@@ -2,8 +2,6 @@
 Module containing the HmmBuild block for the EAPM plugin as a nord3 implementation
 """
 
-import os
-
 from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # ==========================#
@@ -45,6 +43,8 @@
 
 def runHmmBuild(block: SlurmBlock):
 
+    import os
+
     input = block.inputs.get("input_msa", None)
 
     if "nord3" not in block.remote.host:
@@ -76,7 +76,12 @@ def runHmmBuild(block: SlurmBlock):
 
     output = block.outputs.get("output", "output.hmm")
 
-    jobs = [f"hmmbuild {folderName}/{output} {folderName}/{input}"]
+    if block.remote.isLocal:
+        hmmerExecutable = block.config.get("hmmer_path", "hmmer") + "/hmmbuild"
+    else:
+        hmmerExecutable = "hmmbuild"
+
+    jobs = [f"{hmmerExecutable} {folderName}/{output} {folderName}/{input}"]
 
     from utils import launchCalculationAction
 
@@ -91,6 +96,8 @@ def runHmmBuild(block: SlurmBlock):
 
 
 def finalAction(block: SlurmBlock):
+    import os
+
     from utils import downloadResultsAction
 
     downloaded_path = downloadResultsAction(block)
diff --git a/EAPM/Include/Blocks/HmmScan.py b/EAPM/Include/Blocks/HmmScan.py
index 7dc939a..208228f 100644
--- a/EAPM/Include/Blocks/HmmScan.py
+++ b/EAPM/Include/Blocks/HmmScan.py
@@ -2,8 +2,6 @@
 Module containing the HmmScan block for the EAPM plugin as a nord3 implementation
 """
 
-import os
-
 from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # ==========================#
@@ -50,6 +48,7 @@
 
 
 def runHmmScan(block: SlurmBlock):
+    import os
 
     input = block.inputs.get("input_fasta", None)
 
@@ -83,7 +82,12 @@ def runHmmScan(block: SlurmBlock):
     hmmDB = block.variables.get("hmm_db", None)
     output = block.outputs.get("output", "output.hmm")
 
-    jobs = [f"hmmscan {hmmDB} {folderName}/{input} -o {folderName}/{output}"]
+    if block.remote.isLocal:
+        hmmerExecutable = block.config.get("hmmer_path", "hmmer") + "/hmmscan"
+    else:
+        hmmerExecutable = "hmmscan"
+
+    jobs = [f"{hmmerExecutable} {hmmDB} {folderName}/{input} -o {folderName}/{output}"]
 
     from utils import launchCalculationAction
 
@@ -98,6 +102,8 @@ def runHmmScan(block: SlurmBlock):
 
 
 def finalAction(block: SlurmBlock):
+    import os
+
     from utils import downloadResultsAction
 
     downloaded_path = downloadResultsAction(block)
diff --git a/EAPM/Include/Blocks/HmmSearch.py b/EAPM/Include/Blocks/HmmSearch.py
index 10d6fb2..4c46c30 100644
--- a/EAPM/Include/Blocks/HmmSearch.py
+++ b/EAPM/Include/Blocks/HmmSearch.py
@@ -2,8 +2,6 @@
 Module containing the HmmSearch block for the EAPM plugin as a nord3 implementation
 """
 
-import os
-
 from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # ==========================#
@@ -58,6 +56,8 @@
 
 def runHmmSearch(block: SlurmBlock):
 
+    import os
+
     input = block.inputs.get("input_hmm", None)
 
     if "nord3" not in block.remote.host:
@@ -94,8 +94,13 @@ def runHmmSearch(block: SlurmBlock):
         "sequence_db", "/gpfs/projects/shared/public/AlphaFold/uniref90/uniref90.fa"
     )
 
+    if block.remote.isLocal:
+        hmmerExecutable = block.config.get("hmmer_path", "hmmer") + "/hmmsearch"
+    else:
+        hmmerExecutable = "hmmsearch"
+
     jobs = [
-        f"hmmsearch --cpu {cpus} -E {evalue} {folderName}/{input} {sequenceDB} -o {folderName}/{output}"
+        f"{hmmerExecutable} --cpu {cpus} -E {evalue} {folderName}/{input} {sequenceDB} -o {folderName}/{output}"
     ]
 
     from utils import launchCalculationAction
@@ -111,6 +116,8 @@ def runHmmSearch(block: SlurmBlock):
 
 
 def finalAction(block: SlurmBlock):
+    import os
+
     from utils import downloadResultsAction
 
     downloaded_path = downloadResultsAction(block)
diff --git a/EAPM/Include/Blocks/HmmSearchLocal.py b/EAPM/Include/Blocks/HmmSearchLocal.py
index bd6da5e..b8eeffa 100644
--- a/EAPM/Include/Blocks/HmmSearchLocal.py
+++ b/EAPM/Include/Blocks/HmmSearchLocal.py
@@ -2,10 +2,7 @@
 Module containing the HmmSearch block for the EAPM plugin as a local implementation
 """
 
-import os
-import pyhmmer
-from HorusAPI import PluginBlock, PluginVariable, VariableTypes, Extensions
-
+from HorusAPI import Extensions, PluginBlock, PluginVariable, VariableTypes
 
 # ==========================#
 # Variable inputs
@@ -38,47 +35,51 @@
     allowedValues=["domtbl"],
 )
 
+
 def runHmmSearch(block: PluginBlock):
-    
+    import os
+
+    import pyhmmer
+
     input = block.inputs.get("input_hmm", None)
-    
+
     if input is None:
         raise Exception("No input hmm provided")
-   
+
     if not os.path.exists(input):
         raise Exception(f"The input hmm file does not exist: {input}")
-    
+
     try:
         with pyhmmer.plan7.HMMFile(input) as hmm_file:
             hmm = hmm_file.read()
     except Exception as e:
         raise Exception(f"Error reading the input hmm file: {e}")
-    
+
     alphabet = pyhmmer.plan7.Alphabet.amino()
     background = pyhmmer.plan7.Background(alphabet)
     pipeline = pyhmmer.plan7.Pipeline(alphabet, background=background)
-    
+
     sequenceDB = block.inputs.get("sequence_db", None)
-    
+
     if sequenceDB is None:
         raise Exception("No sequence database provided")
-    
+
     if not os.path.exists(sequenceDB):
         raise Exception(f"The sequence database file does not exist: {sequenceDB}")
-    
+
     try:
         with pyhmmer.easel.SequenceFile(sequenceDB, digital=True, alphabet=alphabet) as seq_file:
             hits = pipeline.search_hmm(hmm, seq_file)
     except Exception as e:
         raise Exception(f"Error searching the sequence database: {e}")
-    
+
     output = block.outputs.get("output", "output.domtbl")
-    
+
     with open(output, "wb") as f:
         hits.write(f, format="domains")
-        
+
     block.setOutput("outputVariable", output)
-    
+
 
 hmmsearchLocalBlock = PluginBlock(
     name="HmmSearch Local",
diff --git a/EAPM/Include/Blocks/JackHmmer.py b/EAPM/Include/Blocks/JackHmmer.py
index f14d47d..b2f01f9 100644
--- a/EAPM/Include/Blocks/JackHmmer.py
+++ b/EAPM/Include/Blocks/JackHmmer.py
@@ -2,8 +2,6 @@
 Module containing the JackHmmer block for the EAPM plugin as a nord3 implementation
 """
 
-import os
-
 from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # ==========================#
@@ -44,17 +42,25 @@
     id="sequence_db",
     name="Sequence DB",
     description="The sequence database to search",
-    type=VariableTypes.STRING,
-    defaultValue="/gpfs/projects/shared/public/AlphaFold/uniref90/uniref90.fa",
+    type=VariableTypes.FILE,
+    defaultValue="/apps/ACC/ALPHAFOLD/SRC/database/Alphafold/uniref90/uniref90.fasta",
+)
+folderNameVar = PluginVariable(
+    id="folder_name",
+    name="Folder name",
+    description="The folder name",
+    type=VariableTypes.FOLDER,
+    defaultValue="jackHmmer",
 )
 
 
 def runJackHmmer(block: SlurmBlock):
+    import os
 
     inputfasta = block.inputs.get("input_fasta", None)
 
-    if "nord3" not in block.remote.host:
-        raise Exception("This block only works on Nord3.")
+    # if "nord3" not in block.remote.host or "glogin" not in block.remote.host:
+    #     raise Exception("This block only works on Nord3 or mn.")
 
     if inputfasta is None:
         raise Exception("No input fasta provided")
@@ -71,7 +77,7 @@ def runJackHmmer(block: SlurmBlock):
 
     if not removeExisting and os.path.exists(folderName):
         raise Exception(
-            "The folder {} already exists. Please, choose another name or remove it.".format(
+            "The folder {} already exists. Please, choose another name or remove it with the RemoveExistingFolder option.".format(
                 folderName
             )
         )
@@ -80,15 +86,19 @@ def runJackHmmer(block: SlurmBlock):
     os.makedirs(folderName, exist_ok=True)
     os.system(f"cp {inputfasta} {folderName}")
 
+    inputfasta = os.path.join(folderName, os.path.basename(inputfasta))
+
     output = block.outputs.get("output", "output.hmm")
     sequenceDB = block.variables.get(
-        "sequence_db", "/gpfs/projects/shared/public/AlphaFold/uniref90/uniref90.fa"
+        "sequence_db", "/apps/ACC/ALPHAFOLD/SRC/database/Alphafold/uniref90/uniref90.fasta"
     )
     cpus = block.variables.get("cpus", 1)
 
-    jobs = [
-        f"jackhmmer -o {folderName}/{output} --cpu {cpus} {folderName}/{inputfasta} {sequenceDB}"
-    ]
+    if block.remote.isLocal:
+        hmmerExecutable = block.config.get("hmmer_path", "hmmer") + "/jackhmmer"
+    else:
+        hmmerExecutable = "jackhmmer"
+    jobs = [f"{hmmerExecutable} -o {folderName}/{output} --cpu {cpus} {inputfasta} {sequenceDB}"]
 
     from utils import launchCalculationAction
 
@@ -103,6 +113,8 @@ def runJackHmmer(block: SlurmBlock):
 
 
 def finalAction(block: SlurmBlock):
+    import os
+
     from utils import downloadResultsAction
 
     downloaded_path = downloadResultsAction(block)
@@ -122,6 +134,6 @@ def finalAction(block: SlurmBlock):
     finalAction=finalAction,
     description="Iteratively search a protein sequence against a protein database",
     inputs=[fastaInput],
-    variables=BSC_JOB_VARIABLES + [sequenceDBVar, removeExistingResults],
+    variables=BSC_JOB_VARIABLES + [sequenceDBVar, removeExistingResults, folderNameVar],
     outputs=[outputVariable],
 )
diff --git a/EAPM/Include/Blocks/MSA2HMM.py b/EAPM/Include/Blocks/MSA2HMM.py
index dcdcf60..d1c0d7d 100644
--- a/EAPM/Include/Blocks/MSA2HMM.py
+++ b/EAPM/Include/Blocks/MSA2HMM.py
@@ -2,11 +2,7 @@
 Module containing the MSA2HMM block for the EAPM plugin
 """
 
-import pyhmmer
-import os
-
-from HorusAPI import PluginBlock, PluginVariable, VariableTypes, VariableGroup
-
+from HorusAPI import PluginBlock, PluginVariable, VariableGroup, VariableTypes
 
 # ==========================#
 # Variable inputs
@@ -44,36 +40,39 @@
 # ==========================#
 
 
-
 def convertMSA2HMM(block: PluginBlock):
     """
     Convert MSA to HMM
     """
+    import os
+
+    import pyhmmer
 
     # Loading plugin variables
     inputMSA = block.inputs.get("input_file_msa")
     if inputMSA is None:
         raise Exception("No input MSA provided")
-    
+
     if not os.path.exists(inputMSA):
         raise Exception(f"The input MSA file does not exist: {inputMSA}")
-    
+
     alphabet = pyhmmer.easel.Alphabet.amino()
-    
+
     with pyhmmer.easel.MSAFile(inputMSA, digital=True, alphabet=alphabet) as msa_file:
         msa = msa_file.read()
         msa.name = b"input_msa"
-    
+
     builder = pyhmmer.plan7.Builder(alphabet)
     background = pyhmmer.plan7.Background(alphabet)
     hmm, _, _ = builder.build_msa(msa, background)
-    
+
     output = "output.hmm"
     with open(output, "wb") as output_file:
         hmm.write(output_file)
-        
+
     block.setOutput("output_hmm", output)
-    
+
+
 convertMSAToHMMBlock = PluginBlock(
     name="MSA to HMM",
     description="Convert MSA files to HMM",
diff --git a/EAPM/Include/Blocks/Mafft.py b/EAPM/Include/Blocks/Mafft.py
index 473c19e..b1e764d 100644
--- a/EAPM/Include/Blocks/Mafft.py
+++ b/EAPM/Include/Blocks/Mafft.py
@@ -2,10 +2,7 @@
 Module containing the Mafft block for the EAPM plugin
 """
 
-import Bio.AlignIO
-import Bio.SeqIO
-
-from HorusAPI import Extensions, PluginBlock, PluginVariable, VariableTypes
+from HorusAPI import PluginBlock, PluginVariable, VariableTypes
 
 # ==========================#
 # Variable inputs
diff --git a/EAPM/Include/Blocks/PDBToMAE.py b/EAPM/Include/Blocks/PDBToMAE.py
index e033459..4f0f6bb 100644
--- a/EAPM/Include/Blocks/PDBToMAE.py
+++ b/EAPM/Include/Blocks/PDBToMAE.py
@@ -1,6 +1,3 @@
-import os
-import shutil
-
 from HorusAPI import PluginBlock, PluginVariable, VariableGroup, VariableTypes
 
 # Input variables
@@ -45,6 +42,9 @@
 
 
 def convertPDBToMAE(block: PluginBlock):
+    import os
+    import shutil
+
     # Test if we have valid glide installation
     command = "echo $SCHRODINGER"
     output = block.remote.remoteCommand(command)
@@ -58,7 +58,23 @@ def convertPDBToMAE(block: PluginBlock):
 
     import prepare_proteins
 
-    pdb_folder = block.inputs.get("pdb_folder", None)
+    if block.selectedInputGroup == singlePDBVariable.id:
+        pdb_file = block.inputs.get("single_pdb", None)
+
+        if pdb_file is None:
+            raise Exception("No PDB file selected")
+
+        if not os.path.isfile(pdb_file):
+            raise Exception(f"Invalid PDB file: {pdb_file}")
+
+        if os.path.exists("tmp_ligand"):
+            shutil.rmtree("tmp_ligand")
+        os.mkdir("tmp_ligand")
+        shutil.copy(pdb_file, "tmp_ligand")
+
+        pdb_folder = os.path.join(os.getcwd(), "tmp_ligand")
+    else:
+        pdb_folder = block.inputs.get("pdb_folder", None)
 
     if pdb_folder is None:
         raise Exception("No PDB folder selected")
@@ -163,12 +179,6 @@ def mockSystem(command):
     name="PDB to MAE",
     description="Convert PDB files to MAE for Glide",
     inputGroups=[
-        VariableGroup(
-            id=structureVariable.id,
-            name=structureVariable.name,
-            description=structureVariable.description,
-            variables=[structureVariable],
-        ),
         VariableGroup(
             id=singlePDBVariable.id,
             name=singlePDBVariable.name,
@@ -181,6 +191,12 @@ def mockSystem(command):
             description=pdbFolderVariable.description,
             variables=[pdbFolderVariable],
         ),
+        VariableGroup(
+            id=structureVariable.id,
+            name=structureVariable.name,
+            description=structureVariable.description,
+            variables=[structureVariable],
+        ),
     ],
     variables=[changeLigandNameVariable],
     outputs=[outputVariable],
diff --git a/EAPM/Include/Blocks/PeleEAPM.py b/EAPM/Include/Blocks/PeleEAPM.py
index ddb9136..636fec9 100644
--- a/EAPM/Include/Blocks/PeleEAPM.py
+++ b/EAPM/Include/Blocks/PeleEAPM.py
@@ -1,4 +1,4 @@
-import random
+
 
 from HorusAPI import (PluginVariable, SlurmBlock, VariableGroup, VariableList,
                       VariableTypes)
@@ -9,7 +9,7 @@
     name="PELE yaml",
     description="YAML file containing the PELE configuration",
     type=VariableTypes.FILE,
-    defaultValue="cst_input.yaml",
+    defaultValue="input.yaml",
     allowedValues=["yaml"],
 )
 
@@ -25,7 +25,7 @@
     id="poses_folder",
     name="Best docking poses",
     description="Best docking poses to analyse",
-    type=VariableTypes.FOLDER
+    type=VariableTypes.FOLDER,
 )
 
 glideOutputVariable = PluginVariable(
@@ -41,7 +41,7 @@
     id="folder_input_group",
     name="Folder input group",
     description="Input the model and ligand folders after a Dcoking Grid setup has been run",
-    variables=[modelFolderVariable, posesFolderVariable, yamlPELEFileVariable]
+    variables=[modelFolderVariable, posesFolderVariable, yamlPELEFileVariable],
 )
 
 glideOutputGroup = VariableGroup(
@@ -168,7 +168,7 @@
     name="PELE separator",
     description="Separator for the PELE models and ligands",
     type=VariableTypes.STRING,
-    defaultValue="-",
+    defaultValue="@",
     category="PELE",
 )
 
@@ -326,7 +326,7 @@
     description="Enable log file",
     type=VariableTypes.BOOLEAN,
     defaultValue=False,
-    category="PELE"
+    category="PELE",
 )
 
 rescoringVariable = PluginVariable(
@@ -335,7 +335,7 @@
     description="Enable rescoring",
     type=VariableTypes.BOOLEAN,
     defaultValue=False,
-    category="PELE"
+    category="PELE",
 )
 
 epsilonVariable = PluginVariable(
@@ -344,7 +344,7 @@
     description="TODO Epsilon description",
     type=VariableTypes.FLOAT,
     defaultValue=0.5,
-    category="PELE"
+    category="PELE",
 )
 
 ligandEquilibrationCstVariable = PluginVariable(
@@ -353,7 +353,7 @@
     description="TODO Ligand equilibration cst description",
     type=VariableTypes.BOOLEAN,
     defaultValue=True,
-    category="PELE"
+    category="PELE",
 )
 
 covalentSetupVariable = PluginVariable(
@@ -362,7 +362,7 @@
     description="Enable covalent setup",
     type=VariableTypes.BOOLEAN,
     defaultValue=False,
-    category="PELE"
+    category="PELE",
 )
 
 nonbondedNewFlagVariable = PluginVariable(
@@ -371,7 +371,7 @@
     description="Enable nonbonded new flag",
     type=VariableTypes.BOOLEAN,
     defaultValue=False,
-    category="PELE"
+    category="PELE",
 )
 
 onlyModelsVariable = PluginVariable(
@@ -414,12 +414,12 @@
     category="PELE",
 )
 
-membraneResiduesVariable= PluginVariable(
+membraneResiduesVariable = PluginVariable(
     id="membrane_residues",
     name="Membrane residues",
     description="TODO membrane residues description",
     type=VariableTypes.LIST,
-    category="PELE"
+    category="PELE",
 )
 
 biasToPointVariable = PluginVariable(
@@ -427,7 +427,7 @@
     name="Bias to point",
     description="TODO bias_to_point description",
     type=VariableTypes.LIST,
-    category="PELE"
+    category="PELE",
 )
 
 comBias1Variable = PluginVariable(
@@ -435,7 +435,7 @@
     name="com bias1",
     description="TODO com_bias1 description",
     type=VariableTypes.LIST,
-    category="PELE"
+    category="PELE",
 )
 
 comBias2Variable = PluginVariable(
@@ -443,7 +443,7 @@
     name="com bias2",
     description="TODO com_bias2 description",
     type=VariableTypes.LIST,
-    category="PELE"
+    category="PELE",
 )
 
 ligandTemplateVariable = PluginVariable(
@@ -478,35 +478,35 @@
     id="model",
     name="Model",
     description="TODO model variable description",
-    type=VariableTypes.STRING
+    type=VariableTypes.STRING,
 )
 
 ligandVariable = PluginVariable(
     id="ligand",
     name="Ligand",
     description="TODO ligand variable description",
-    type=VariableTypes.STRING
+    type=VariableTypes.STRING,
 )
 
 chainVariable = PluginVariable(
     id="chain",
     name="Chain",
     description="TODO chain variable description",
-    type=VariableTypes.STRING
+    type=VariableTypes.STRING,
 )
 
 residueVariable = PluginVariable(
     id="residue",
     name="Residue number",
     description="TODO residue number variable description",
-    type=VariableTypes.INTEGER
+    type=VariableTypes.INTEGER,
 )
 
 atomNameVariable = PluginVariable(
     id="atom_name",
     name="Atom name",
     description="TODO atom name variable description",
-    type=VariableTypes.STRING
+    type=VariableTypes.STRING,
 )
 
 # box_centers VariableList
@@ -515,13 +515,7 @@
     name="Box centers",
     description="TODO Box center variable description",
     category="PELE",
-    prototypes=[
-        modelVariable,
-        ligandVariable,
-        chainVariable,
-        residueVariable,
-        atomNameVariable
-    ],
+    prototypes=[modelVariable, ligandVariable, chainVariable, residueVariable, atomNameVariable],
 )
 
 # Outputs
@@ -533,9 +527,13 @@
 )
 
 
-
 def peleAction(block: SlurmBlock):
     if block.selectedInputGroup == "glide_output_group":
+        glide_outputr = block.inputs.get("glide_output")
+        # load the pickle file
+
+        # with open(glide_outputr, "rb") as f:
+        #     glide_output = pickle.load(f)
         glide_output = block.inputs.get("glide_output")
         poses_folder = glide_output.get("poses_folder")
         models_folder = glide_output.get("models_folder")
@@ -549,7 +547,7 @@ def peleAction(block: SlurmBlock):
         atom_pairs = {}
 
     # Get all the variables from the block
-    boxCentersValue = block.variables.get("box_centers", [])
+    boxCentersValue = block.variables.get("box_centers", None)
     boxRadiusValue = block.variables.get("box_radius", 10)
     constraintsValue = block.variables.get("constraints", [])
     ligandIndexValue = block.variables.get("ligand_index", 1)
@@ -558,7 +556,7 @@ def peleAction(block: SlurmBlock):
     peleIterationsValue = block.variables.get("pele_iterations", 5)
     equilibrationStepsValue = block.variables.get("equilibration_steps", 100)
     ligandEnergyGroupsValue = block.variables.get("ligand_energy_groups", [])
-    peleSeparatorValue = block.variables.get("pele_separator", "-")
+    peleSeparatorValue = block.variables.get("pele_separator", "@")
     usePeleffyValue = block.variables.get("use_peleffy", True)
     useSrunValue = block.variables.get("use_srun", True)
     energyByResidueValue = block.variables.get("energy_by_residue", False)
@@ -579,7 +577,7 @@ def peleAction(block: SlurmBlock):
     onlyModelsValue = block.variables.get("only_models", [])
     onlyLigandsValue = block.variables.get("only_ligands", [])
     onlyCombinationsValue = block.variables.get("only_combinations", [])
-    nonbondedEnergyValue = block.variables.get('nonbonded_energy', {})
+    nonbondedEnergyValue = block.variables.get("nonbonded_energy", {})
     ligandTemplateValue = block.variables.get("ligand_template", "")
     seedValue = block.variables.get("seed", -1)
     logFileValue = block.variables.get("log_file", False)
@@ -595,19 +593,31 @@ def peleAction(block: SlurmBlock):
     comBias2Value = block.variables.get("com_bias2", {})
 
     # Parse spawningValue
-    validSpawnings = ['independent', 'inverselyProportional', 'epsilon', 'variableEpsilon',
-                    'independentMetric', 'UCB', 'FAST', 'ProbabilityMSM', 'MetastabilityMSM',
-                    'IndependentMSM']
-    
+    validSpawnings = [
+        "independent",
+        "inverselyProportional",
+        "epsilon",
+        "variableEpsilon",
+        "independentMetric",
+        "UCB",
+        "FAST",
+        "ProbabilityMSM",
+        "MetastabilityMSM",
+        "IndependentMSM",
+    ]
+
     if spawningValue != None and spawningValue not in validSpawnings:
-            message = 'Spawning method %s not found.' % spawningValue
-            message = 'Allowed options are: ' + str(validSpawnings)
-            raise ValueError(message)
+        message = "Spawning method %s not found." % spawningValue
+        message = "Allowed options are: " + str(validSpawnings)
+        raise ValueError(message)
 
     # Parse energyByResidueValue
-    energy_by_residue_types = ['all', 'lennard_jones', 'sgb', 'electrostatic']
+    energy_by_residue_types = ["all", "lennard_jones", "sgb", "electrostatic"]
     if energyByResidueTypeValue not in energy_by_residue_types:
-        raise ValueError('%s not found. Try: %s' % (energyByResidueTypeValue, energy_by_residue_types))
+        raise ValueError(
+            "%s not found. Try: %s" % (energyByResidueTypeValue, energy_by_residue_types)
+        )
+    import random
 
     # Parse seedValue
     if seedValue == -1:
@@ -616,44 +626,49 @@ def peleAction(block: SlurmBlock):
     # Parse ligandEnergyGroups
     if not isinstance(ligandEnergyGroupsValue, type(None)):
         if not isinstance(ligandEnergyGroupsValue, dict):
-            raise ValueError('Ligand energy groups, must be given as a dictionary')
-        
-    # Parse box_centers
+            raise ValueError("Ligand energy groups, must be given as a dictionary")
 
-    box_centers = {}
-    for model in boxCentersValue:
-        box_centers[(model['model'], model['ligand'])] = (model['chain'], model['residue'], model['atom_name'])
+    # Parse box_centers
+    if not isinstance(boxCentersValue, type(None)) or boxCentersValue is not None:
+        box_centers = {}
+        for model in boxCentersValue:
+            box_centers[(model["model"], model["ligand"])] = (
+                model["chain"],
+                model["residue"],
+                model["atom_name"],
+            )
+    else:
+        box_centers = None
 
     # Parse skip_models
     if not isinstance(skipModelsValue, type(None)):
         if not isinstance(skipModelsValue, list):
-            raise ValueError('skip_models must be a list.')
+            raise ValueError("skip_models must be a list.")
 
-    
     # Parse skip_ligands
     if not isinstance(skipLigandsValue, type(None)):
         if not isinstance(skipLigandsValue, list):
-            raise ValueError('skip_ligands must be a list.')
+            raise ValueError("skip_ligands must be a list.")
 
     # Parse nonbonded_energy
     if not isinstance(nonbondedEnergyValue, type(None)):
         if not isinstance(nonbondedEnergyValue, dict):
-            raise ValueError('nonbonded_energy, must be given as a dictionary')
+            raise ValueError("nonbonded_energy, must be given as a dictionary")
 
     # Parse only_ligands
     if not isinstance(onlyLigandsValue, type(None)):
         if not isinstance(onlyLigandsValue, list):
-            raise ValueError('only_ligands must be a list.')
-    
+            raise ValueError("only_ligands must be a list.")
+
     # Parse only_models
     if not isinstance(onlyModelsValue, type(None)):
         if not isinstance(onlyModelsValue, list):
-            raise ValueError('only_models must be a list.')
+            raise ValueError("only_models must be a list.")
 
     # Parse only_combinations
     if not isinstance(onlyCombinationsValue, type(None)):
         if not isinstance(onlyCombinationsValue, list):
-            raise ValueError('only_combinations must be a list.')
+            raise ValueError("only_combinations must be a list.")
 
     import prepare_proteins
 
@@ -663,7 +678,7 @@ def peleAction(block: SlurmBlock):
     selections = block.variables.get("selections_list", [])
     if atom_pairs == {}:
         groups = []
-        for model in models:  
+        for model in models:
             atom_pairs[model] = {}
             for selection in selections:
                 current_group = selection["group"]
@@ -686,7 +701,7 @@ def peleAction(block: SlurmBlock):
                     atom_pairs[model][ligandName] = []
                 atom_pairs[model][ligandName].append((protein_tuple, ligand_atom))
 
-    cst_yaml = block.inputs.get("yaml_pele_file")
+    input_yaml = block.inputs.get("yaml_pele_file")
 
     cpus = block.variables.get("cpus", 48)
     peleFolderName = block.variables.get("pele_folder_name", "pele")
@@ -694,7 +709,7 @@ def peleAction(block: SlurmBlock):
     jobs = models.setUpPELECalculation(
         peleFolderName,
         poses_folder,
-        cst_yaml,
+        input_yaml,
         box_radius=boxRadiusValue,
         iterations=peleIterationsValue,
         cpus=cpus,
@@ -738,7 +753,7 @@ def peleAction(block: SlurmBlock):
         bias_to_point=biasToPointValue,
         com_bias1=comBias1Value,
         com_bias2=comBias2Value,
-        ligand_energy_groups=ligandEnergyGroupsValue
+        ligand_energy_groups=ligandEnergyGroupsValue,
     )
 
     from utils import launchCalculationAction
@@ -754,7 +769,7 @@ def peleAction(block: SlurmBlock):
     )
 
 
-def peleFinalAction(block: SlurmBlock):#
+def peleFinalAction(block: SlurmBlock):  #
     print("Pele finished")
 
     from utils import downloadResultsAction
@@ -766,7 +781,6 @@ def peleFinalAction(block: SlurmBlock):#
     block.setOutput("pele_output_folder", peleFolderName)
 
 
-
 from utils import BSC_JOB_VARIABLES
 
 blockVariables = BSC_JOB_VARIABLES + [
@@ -813,18 +827,20 @@ def peleFinalAction(block: SlurmBlock):#
     membraneResiduesVariable,
     biasToPointVariable,
     comBias1Variable,
-    comBias2Variable
-
+    comBias2Variable,
 ]
 
+
 def wrappedFunction(block: SlurmBlock):
     try:
         peleAction(block)
     except Exception as e:
         import traceback
+
         print("Exception:", e)
         traceback.print_exc()
 
+
 peleBlock = SlurmBlock(
     name="PELE",
     description="Run PELE",
diff --git a/EAPM/Include/Blocks/PrepWizardEAPM.py b/EAPM/Include/Blocks/PrepWizardEAPM.py
index 08e903a..70774a2 100644
--- a/EAPM/Include/Blocks/PrepWizardEAPM.py
+++ b/EAPM/Include/Blocks/PrepWizardEAPM.py
@@ -2,9 +2,7 @@
 Module containing the PrepWizard block for the EAPM plugin
 """
 
-import os
-
-from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
+from HorusAPI import PluginVariable, SlurmBlock, VariableGroup, VariableTypes
 
 # ==========================#
 # Variable inputs
@@ -16,6 +14,26 @@
     type=VariableTypes.FOLDER,
     defaultValue=None,
 )
+inputFilePW = PluginVariable(
+    name="Input File",
+    id="input_file",
+    description="File of the pdb to prepare.",
+    type=VariableTypes.FILE,
+    allowedValues=["pdb"],
+)
+folderVariableGroup = VariableGroup(
+    id="folder_variable_group",
+    name="Folder variable group",
+    description="Input folder with the models.",
+    variables=[inputFolderPW],
+)
+fileVariableGroup = VariableGroup(
+    id="file_output_variable_group",
+    name="PDB file group",
+    description="Input PDB file.",
+    variables=[inputFilePW],
+)
+
 
 # ==========================#
 # Variable outputs
@@ -26,6 +44,13 @@
     description="Folder containing the prepared proteins.",
     type=VariableTypes.FOLDER,
 )
+outputPDB = PluginVariable(
+    name="Output PDB",
+    id="out_pdb",
+    description="Last PDB of the Prepwizard.",
+    type=VariableTypes.FILE,
+    allowedValues=["pdb"],
+)
 
 ##############################
 # Block's advanced variables #
@@ -39,6 +64,7 @@
 )
 
 
+# Variables
 phPW = PluginVariable(
     name="PH",
     id="ph",
@@ -112,28 +138,36 @@ def prepWizardAction(block: SlurmBlock):
     Args:
         block (SlurmBlock): The block to run the action on.
     """
-    # Loading plugin variables
-    inputFolder = block.inputs.get("input_folder", None)
-    if inputFolder is None:
-        raise Exception("No input folder provided.")
+
+    import os
+
+    if block.selectedInputGroup == fileVariableGroup.id:
+        input_file = block.inputs.get(inputFilePW.id, None)
+        input_folder = "models"
+        os.makedirs(input_folder, exist_ok=True)
+        os.system(f"cp {input_file} {input_folder}")
+    elif block.selectedInputGroup == folderVariableGroup.id:
+        input_folder = block.inputs.get(inputFolderPW.id, None)
+    else:
+        raise Exception("No input selected")
 
     # Get prepWizard variables
-    folderName = block.variables.get("folder_name", "prepared_proteins")
-    ph = int(block.variables.get("ph", 7))
-    epikPH = block.variables.get("epik_ph", False)
-    sampleWater = block.variables.get("sample_water", False)
-    removeHydrogens = block.variables.get("remove_hydrogens", False)
-    delWaterHbondCutOff = block.variables.get("del_water_hbond_cut_off", False)
-    fillLoops = block.variables.get("fill_loops", False)
-    protonationStates = block.variables.get("protonation_states", None)
-    noepik = block.variables.get("no_epik", False)
-    noProtAssign = block.variables.get("no_prot_assign", False)
+    folderName = block.variables.get(folderNameVariable.id, "prepared_proteins")
+    ph = int(block.variables.get(phPW.id, 7))
+    epikPH = block.variables.get(epikPHPW.id, False)
+    sampleWater = block.variables.get(sampleWaterPW.id, False)
+    removeHydrogens = block.variables.get(removeHydrogensPW.id, False)
+    delWaterHbondCutOff = block.variables.get(delWaterHbondCutOffPW.id, False)
+    fillLoops = block.variables.get(fillLoopsPW.id, False)
+    protonationStates = block.variables.get(protonationStatesPW.id, None)
+    noepik = block.variables.get(noepikPW.id, False)
+    noProtAssign = block.variables.get(noProtAssignPW.id, False)
 
     import prepare_proteins
 
     print("Loading pdbs files...")
 
-    models = prepare_proteins.proteinModels(inputFolder)
+    models = prepare_proteins.proteinModels(input_folder)
 
     print("Setting up PrepWizard Optimitzations...")
 
@@ -173,11 +207,13 @@ def prepWizardAction(block: SlurmBlock):
 
 
 def downloadPrepWizardResults(block: SlurmBlock):
+    import os
+
     from utils import downloadResultsAction
 
     downloadResultsAction(block)
 
-    folderName = block.variables.get("folder_name", "prepared_proteins")
+    folderName = block.variables.get(folderNameVariable.id, "prepared_proteins")
 
     # Create the output folder containing the prepared proteins
     if not os.path.exists(folderName):
@@ -193,7 +229,8 @@ def downloadPrepWizardResults(block: SlurmBlock):
                 pdbPath = os.path.join(folderName + "_wizard", "output_models", model, file)
                 shutil.copyfile(pdbPath, finalPath)
 
-    block.setOutput("prepared_proteins", folderName)
+    block.setOutput(outputPDB.id, finalPath)
+    block.setOutput(outputPW.id, folderName)
 
 
 from utils import BSC_JOB_VARIABLES
@@ -218,6 +255,6 @@ def downloadPrepWizardResults(block: SlurmBlock):
     initialAction=prepWizardAction,
     finalAction=downloadPrepWizardResults,
     variables=block_variables,
-    inputs=[inputFolderPW],
-    outputs=[outputPW],
+    inputGroups=[folderVariableGroup, fileVariableGroup],
+    outputs=[outputPDB, outputPW],
 )
diff --git a/EAPM/Include/Blocks/Rbcavity.py b/EAPM/Include/Blocks/Rbcavity.py
new file mode 100644
index 0000000..04b89ac
--- /dev/null
+++ b/EAPM/Include/Blocks/Rbcavity.py
@@ -0,0 +1,93 @@
+"""
+Module containing the rbcavity block for the EAPM plugin
+"""
+
+from HorusAPI import PluginBlock, PluginVariable, VariableTypes
+
+# ==========================#
+# Variable inputs
+# ==========================#
+inputPRMFile = PluginVariable(
+    name="Parameter file",
+    id="input_prm_file",
+    description="The input '.prm' file.",
+    type=VariableTypes.FILE,
+    defaultValue="parameter_file.prm",
+    allowedValues=["prm"],
+)
+
+# ==========================#
+# Variable outputs
+# ==========================#
+outputLog = PluginVariable(
+    name="Output log",
+    id="output_log",
+    description="The output log file.",
+    type=VariableTypes.FILE,
+    defaultValue="parameter_file.log",
+)
+
+
+##############################
+#       Other variables      #
+##############################
+was = PluginVariable(
+    name="Was",
+    id="was",
+    description="Write docking cavities (plus distance grid) to .as file.",
+    type=VariableTypes.BOOLEAN,
+    defaultValue=True,
+)
+dumpInsight = PluginVariable(
+    name="Dump Insight",
+    id="dump_insight",
+    description="Dump InsightII/PyMOL grids for each cavity for visualisation.",
+    type=VariableTypes.BOOLEAN,
+    defaultValue=False,
+)
+
+
+# Align action block
+def initialRbcavity(block: PluginBlock):
+
+    if block.remote.name != "Local":
+        raise Exception("This block is only available for local execution.")
+
+    # Loading plugin variables
+    input_PRMfile = block.inputs.get(inputPRMFile.id, None)
+    output_log = block.outputs.get(outputLog.id, "parameter_file.log")
+
+    # rbcavity -was -d -r parameter_file.prm > parameter_file.log
+    command = "rbcavity "
+    if block.variables.get("was", True):
+        command += "-was "
+    if block.variables.get("dump_insight", False):
+        command += "-d "
+    command += f"-r {input_PRMfile} > {output_log}"
+
+    print("Setting output of block to the results directory...")
+
+    # subprocess the command
+    import subprocess
+
+    completed_process = subprocess.run(command, shell=True, capture_output=True, text=True)
+
+    # Get the output and error
+    output = completed_process.stdout
+    error = completed_process.stderr
+
+    # Set the output
+    block.setOutput(outputLog.id, output_log)
+
+
+rbCavityBlock = PluginBlock(
+    name="Rbcavity",
+    description="Calculate docking cavities. (For local)",
+    action=initialRbcavity,
+    variables=[
+        was,
+        dumpInsight,
+    ],
+    inputs=[inputPRMFile],
+    outputs=[outputLog],
+)
diff --git a/EAPM/Include/Blocks/Rbdock.py b/EAPM/Include/Blocks/Rbdock.py
new file mode 100644
index 0000000..38d0124
--- /dev/null
+++ b/EAPM/Include/Blocks/Rbdock.py
@@ -0,0 +1,128 @@
+"""
+Module containing the rbdock block for the EAPM plugin
+"""
+
+from HorusAPI import PluginBlock, PluginVariable, VariableTypes
+
+# ==========================#
+# Variable inputs
+# ==========================#
+inputPRMFile = PluginVariable(
+    name="Parameter file",
+    id="input_prm_file",
+    description="The input '.prm' file.",
+    type=VariableTypes.FILE,
+    defaultValue="parameter_file.prm",
+    allowedValues=["prm"],
+)
+inputLigand = PluginVariable(
+    name="Ligand SD file",
+    id="input_ligand",
+    description="The input ligand SD file.",
+    type=VariableTypes.FILE,
+    allowedValues=["sd"],
+)
+
+# ==========================#
+# Variable outputs
+# ==========================#
+outputFile = PluginVariable(
+    name="Output File",
+    id="output_file",
+    description="The output file with the ligand docked.",
+    type=VariableTypes.FILE,
+    defaultValue="parameter_file",
+)
+
+
+##############################
+#       Other variables      #
+##############################
+protoPrmFile = PluginVariable(
+    name="proto Prm File",
+    id="proto_prm_file",
+    description="The docking protocol parameter file.",
+    type=VariableTypes.FILE,
+    defaultValue="dock.prm",
+)
+nRuns = PluginVariable(
+    name="nRuns",
+    id="n_runs",
+    description="Number of runs/ligand (default=1).",
+    type=VariableTypes.INTEGER,
+    defaultValue=None,
+)
+allH = PluginVariable(
+    name="allH",
+    id="all_h",
+    description="Keep all hydrogens, read all hydrogens present (default=polar hydrogens only).",
+    type=VariableTypes.BOOLEAN,
+    defaultValue=False,
+)
+
+
+# Align action block
+def initialRbdock(block: PluginBlock):
+
+    import os
+
+    if block.remote.name != "Local":
+        raise Exception("This block is only available for local execution.")
+
+    # Loading plugin variables
+    input_PRMfile = block.inputs.get(inputPRMFile.id, None)
+    if input_PRMfile is None:
+        raise Exception("No parameter file provided.")
+    if not os.path.exists(input_PRMfile):
+        raise Exception("Parameter file does not exist.")
+    input_ligand = block.inputs.get(inputLigand.id, None)
+    out = "output_dock"
+    if input_ligand is None:
+        raise Exception("No ligand file provided.")
+    if not os.path.exists(input_ligand):
+        raise Exception("Ligand file does not exist.")
+    else:
+        out = os.path.basename(input_ligand).split(".")[0] + "_out"
+    output_file = block.outputs.get(outputFile.id, out)
+
+    # rbcavity -was -d -r parameter_file.prm > parameter_file.log
+    command = f"rbdock -i {input_ligand} -o {output_file} -r {input_PRMfile} "
+    if block.variables.get("proto_prm_file", None) is not None:
+        command += f"-p {block.variables.get('proto_prm_file')} "
+    if block.variables.get("n_runs", None) is not None:
+        command += f"-n {block.variables.get('n_runs')} "
+    if block.variables.get("all_h", False):
+        command += "-allH "
+
+    print("Setting output of block to the results directory...")
+
+    # Subprocess the command
+    import subprocess
+
+    completed_process = subprocess.run(command, shell=True, capture_output=True, text=True)
+
+    # Get the output and error
+    output = completed_process.stdout
+    # Save the output and error
+    with open(f"{output_file}.out", "w") as f:
+        f.write(output)
+    error = completed_process.stderr
+    with open(f"{output_file}.err", "w") as f:
+        f.write(error)
+
+    # Set the output
+    block.setOutput(outputFile.id, output_file)
+
+
+rbDockBlock = PluginBlock(
+    name="Rbdock",
+    description="Calculate the docking. (For local)",
+    action=initialRbdock,
+    variables=[
+        protoPrmFile,
+        nRuns,
+        allH,
+    ],
+    inputs=[inputPRMFile, inputLigand],
+    outputs=[outputFile],
+)
diff --git a/EAPM/Include/Blocks/SetupDockingGrid.py b/EAPM/Include/Blocks/SetupDockingGrid.py
index 4a41dfd..73b3898 100644
--- a/EAPM/Include/Blocks/SetupDockingGrid.py
+++ b/EAPM/Include/Blocks/SetupDockingGrid.py
@@ -1,6 +1,4 @@
-import os
-
-from HorusAPI import InputBlock, PluginVariable, SlurmBlock, VariableGroup, VariableTypes
+from HorusAPI import PluginVariable, SlurmBlock, VariableGroup, VariableTypes
 
 # Input variables
 modelFolderVariable = PluginVariable(
@@ -45,6 +43,8 @@
 
 # Action
 def glideDocking(block: SlurmBlock):
+    import os
+
     import prepare_proteins
 
     models_folder = block.inputs.get("model_folder")
diff --git a/EAPM/Include/Blocks/SetupGlide.py b/EAPM/Include/Blocks/SetupGlide.py
index 1107585..908875e 100644
--- a/EAPM/Include/Blocks/SetupGlide.py
+++ b/EAPM/Include/Blocks/SetupGlide.py
@@ -1,6 +1,3 @@
-import os
-import shutil
-
 from HorusAPI import PluginVariable, SlurmBlock, VariableGroup, VariableTypes
 
 # Input variables
@@ -54,6 +51,9 @@
 
 
 def setupGlideDocking(block: SlurmBlock):
+    import os
+    import shutil
+
     import prepare_proteins
 
     if block.selectedInputGroup == "folder_input_group":
@@ -138,6 +138,8 @@ def setupGlideDocking(block: SlurmBlock):
 
 
 def downloadGlideDocking(block: SlurmBlock):
+    import os
+
     from utils import downloadResultsAction
 
     downloadResultsAction(block)
diff --git a/EAPM/Include/Blocks/TrimAlphafoldModels.py b/EAPM/Include/Blocks/TrimAlphafoldModels.py
index 2d96444..a24eae0 100644
--- a/EAPM/Include/Blocks/TrimAlphafoldModels.py
+++ b/EAPM/Include/Blocks/TrimAlphafoldModels.py
@@ -1,6 +1,3 @@
-import os
-import shutil
-
 from HorusAPI import PluginBlock, PluginVariable, VariableTypes
 
 resultsFolderAF = PluginVariable(
@@ -37,6 +34,8 @@
 
 
 def trimAlphaFoldModels(block: PluginBlock):
+    import os
+    import shutil
 
     # Get the models folder
     models_folder = block.inputs.get("results_folder", None)
diff --git a/EAPM/Include/Blocks/testBlock.py b/EAPM/Include/Blocks/testBlock.py
index 36b14cb..ded4d28 100644
--- a/EAPM/Include/Blocks/testBlock.py
+++ b/EAPM/Include/Blocks/testBlock.py
@@ -1,6 +1,3 @@
-import os
-import shutil
-
 from HorusAPI import PluginBlock, PluginVariable, VariableTypes
 
 # ==========================#
@@ -43,6 +40,8 @@
 
 
 def finalAlhafoldAction(block: PluginBlock):
+    import os
+    import shutil
 
     resultsFolder = "alphafold"
     downloaded_path = "/home/perry/data/acanella/testHorus/all_test/alphafold"
diff --git a/EAPM/Include/Configs/hmmerConfig.py b/EAPM/Include/Configs/hmmerConfig.py
index b3c5322..451b6e2 100644
--- a/EAPM/Include/Configs/hmmerConfig.py
+++ b/EAPM/Include/Configs/hmmerConfig.py
@@ -18,7 +18,7 @@ def checkHmmerInstallation(block: PluginConfig):
     hmmerPath = block.variables.get(hmmerPathVariable.id)
 
     # Check if the path is valid
-    if not os.path.isfile(hmmerPath):
+    if not os.path.isdir(hmmerPath):
         raise Exception("The HMMER executable path is not valid")
 
 
diff --git a/EAPM/Include/utils.py b/EAPM/Include/utils.py
index 9201443..87dc0ac 100644
--- a/EAPM/Include/utils.py
+++ b/EAPM/Include/utils.py
@@ -4,8 +4,7 @@
 import subprocess
 import typing
 
-from HorusAPI import (PluginBlock, PluginVariable, SlurmBlock, VariableList,
-                      VariableTypes)
+from HorusAPI import PluginBlock, PluginVariable, SlurmBlock, VariableList, VariableTypes
 
 localIPs = {"cactus": "84.88.51.217", "blossom": "84.88.51.250", "bubbles": "84.88.51.219"}
 
@@ -36,7 +35,7 @@ def setup_bsc_calculations_based_on_horus_remote(
     if program == "pele":
         if cluster not in [
             "glogin1.bsc.es",
-            "glogin4.bsc.es",
+            "glogin2.bsc.es",
             "glogin3.bsc.es",
             "glogin4.bsc.es",
             "nord3.bsc.es",
@@ -121,7 +120,7 @@ def setup_bsc_calculations_based_on_horus_remote(
             program=program,
             script_name=scriptName,
             cpus=cpus,
-            #module_purge=modulePurge,
+            # module_purge=modulePurge,
         )
     # powerpuff
     elif cluster == "powerpuff":
diff --git a/EAPM/config/eapm.json b/EAPM/config/eapm.json
index e4550b8..f9593d4 100644
--- a/EAPM/config/eapm.json
+++ b/EAPM/config/eapm.json
@@ -1,4 +1,4 @@
 {
     "mafft_path": "/home/perry/miniconda3/envs/horus/bin/mafft",
-    "hmmer_path": "/gpfs/projects/bsc72/conda_envs/hmm/bin/hmmsearch"
+    "hmmer_path": "/home/perry/miniconda3/envs/horus/bin"
 }
\ No newline at end of file
diff --git a/EAPM/preinst.sh b/EAPM/preinst.sh
index b19f3b8..f33cc76 100644
--- a/EAPM/preinst.sh
+++ b/EAPM/preinst.sh
@@ -1,3 +1,3 @@
-pip install "pycaret[analysis, models]" --target deps
+# pip install "pycaret[analysis, models]" --target deps
 
-pip install "werkzeug<=2.3.0"
+# pip install "werkzeug<=2.3.0"