diff --git a/mdagent/mainagent/agent.py b/mdagent/mainagent/agent.py
index 0e20df8c..6f8d7f3b 100644
--- a/mdagent/mainagent/agent.py
+++ b/mdagent/mainagent/agent.py
@@ -7,7 +7,7 @@
 from mdagent.subagents import SubAgentSettings
 from mdagent.utils import PathRegistry, _make_llm
 
-from ..tools import make_all_tools
+from ..tools import get_tools, make_all_tools
 from .prompt import openaifxn_prompt, structured_prompt
 
 load_dotenv()
@@ -35,7 +35,7 @@ class MDAgent:
     def __init__(
         self,
         tools=None,
-        agent_type="OpenAIFunctionsAgent",  # this can also be strucured_chat
+        agent_type="OpenAIFunctionsAgent",  # this can also be structured_chat
         model="gpt-4-1106-preview",  # current name for gpt-4 turbo
         tools_model="gpt-4-1106-preview",
         temp=0.1,
@@ -45,14 +45,16 @@ def __init__(
         subagents_model="gpt-4-1106-preview",
         ckpt_dir="ckpt",
         resume=False,
-        top_k_tools=10,
+        top_k_tools=20,  # set "all" if you want to use all tools (& skills if resume)
         use_human_tool=False,
     ):
         if path_registry is None:
             path_registry = PathRegistry.get_instance()
-        if tools is None:
-            tools_llm = _make_llm(tools_model, temp, verbose)
-            tools = make_all_tools(tools_llm, human=use_human_tool)
+        self.agent_type = agent_type
+        self.user_tools = tools
+        self.tools_llm = _make_llm(tools_model, temp, verbose)
+        self.top_k_tools = top_k_tools
+        self.use_human_tool = use_human_tool
 
         self.llm = ChatOpenAI(
             temperature=temp,
@@ -61,11 +63,7 @@ def __init__(
             streaming=True,
             callbacks=[StreamingStdOutCallbackHandler()],
         )
-        self.agent = AgentExecutor.from_agent_and_tools(
-            tools=tools,
-            agent=AgentType.get_agent(agent_type).from_llm_and_tools(self.llm, tools),
-            handle_parsing_errors=True,
-        )
+
         # assign prompt
         if agent_type == "Structured":
             self.prompt = structured_prompt
@@ -80,9 +78,37 @@ def __init__(
             verbose=verbose,
             ckpt_dir=ckpt_dir,
             resume=resume,
-            retrieval_top_k=top_k_tools,
+        )
+
+    def _initialize_tools_and_agent(self, user_input=None):
+        """Retrieve tools and initialize the agent."""
+        if self.user_tools is not None:
+            self.tools = self.user_tools
+        else:
+            if self.top_k_tools != "all" and user_input is not None:
+                # retrieve only tools relevant to user input
+                self.tools = get_tools(
+                    query=user_input,
+                    llm=self.tools_llm,
+                    subagent_settings=self.subagents_settings,
+                    human=self.use_human_tool,
+                )
+            else:
+                # retrieve all tools, including new tools if any
+                self.tools = make_all_tools(
+                    self.tools_llm,
+                    subagent_settings=self.subagents_settings,
+                    human=self.use_human_tool,
+                )
+        return AgentExecutor.from_agent_and_tools(
+            tools=self.tools,
+            agent=AgentType.get_agent(self.agent_type).from_llm_and_tools(
+                self.llm,
+                self.tools,
+            ),
+            handle_parsing_errors=True,
         )
 
     def run(self, user_input, callbacks=None):
-        # todo: check this for both agent types
+        self.agent = self._initialize_tools_and_agent(user_input)
         return self.agent.run(self.prompt.format(input=user_input), callbacks=callbacks)
diff --git a/mdagent/tools/maketools.py b/mdagent/tools/maketools.py
index 2009dc3a..17daab31 100644
--- a/mdagent/tools/maketools.py
+++ b/mdagent/tools/maketools.py
@@ -123,22 +123,25 @@ def get_tools(
     query,
     llm: BaseLanguageModel,
     subagent_settings: Optional[SubAgentSettings] = None,
-    ckpt_dir="ckpt",
-    retrieval_top_k=10,
+    top_k_tools=15,
     subagents_required=True,
     human=False,
 ):
+    if subagent_settings:
+        ckpt_dir = subagent_settings.ckpt_dir
+    else:
+        ckpt_dir = "ckpt"
+
     retrieved_tools = []
     if subagents_required:
         # add subagents-related tools by default
-        PathRegistry.get_instance()
         retrieved_tools = [
             CreateNewTool(subagent_settings=subagent_settings),
             RetryExecuteSkill(subagent_settings=subagent_settings),
             SkillRetrieval(subagent_settings=subagent_settings),
             WorkflowPlan(subagent_settings=subagent_settings),
         ]
-        retrieval_top_k -= len(retrieved_tools)
+        top_k_tools -= len(retrieved_tools)
         all_tools = make_all_tools(
             llm, subagent_settings, skip_subagents=True, human=human
         )
@@ -163,7 +166,7 @@ def get_tools(
         vectordb.persist()
 
     # retrieve 'k' tools
-    k = min(retrieval_top_k, vectordb._collection.count())
+    k = min(top_k_tools, vectordb._collection.count())
     if k == 0:
         return None
     docs = vectordb.similarity_search(query, k=k)
@@ -173,7 +176,8 @@ def get_tools(
             retrieved_tools.append(all_tools[index])
         else:
             print(f"Invalid index {index}.")
-            print(f"Try deleting vectordb at {ckpt_dir}/all_tools_vectordb.")
+            print("Some tools may be duplicated.")
+            print(f"Try to delete vector DB at {ckpt_dir}/all_tools_vectordb.")
     return retrieved_tools
 
 
@@ -217,7 +221,7 @@ def get_all_tools_string(self):
             all_tools_string += f"{tool.name}: {tool.description}\n"
         return all_tools_string
 
-    def _run(self, task, orig_prompt, curr_tools, execute, args=None):
+    def _run(self, task, orig_prompt, curr_tools, execute=True, args=None):
         # run iterator
         try:
             all_tools_string = self.get_all_tools_string()
diff --git a/notebooks/.DS_Store b/notebooks/.DS_Store
deleted file mode 100644
index 78ff399b..00000000
Binary files a/notebooks/.DS_Store and /dev/null differ