From c0d23e61db8bf75ce3514a9aa5405ceee405a6ee Mon Sep 17 00:00:00 2001
From: cassandra <cassandramasschelein@gmail.com>
Date: Fri, 8 May 2026 13:05:01 +0200
Subject: [PATCH 01/14] added launch mods plus scripts

---
 Launch_scripts/cscs_launch.sh        |  91 +++
 Launch_scripts/systems.csv           | 992 +++++++++++++++++++++++++++
 Launch_scripts/workstation_launch.sh |  76 ++
 src/agents/md_agent.py               |  11 +-
 src/agents/prep_agent.py             |  11 +-
 5 files changed, 1172 insertions(+), 9 deletions(-)
 create mode 100644 Launch_scripts/cscs_launch.sh
 create mode 100644 Launch_scripts/systems.csv
 create mode 100755 Launch_scripts/workstation_launch.sh

diff --git a/Launch_scripts/cscs_launch.sh b/Launch_scripts/cscs_launch.sh
new file mode 100644
index 0000000..5edd63f
--- /dev/null
+++ b/Launch_scripts/cscs_launch.sh
@@ -0,0 +1,91 @@
+#!/bin/bash
+#SBATCH --account=a131
+#SBATCH --partition=debug
+#SBATCH --job-name=dynamate
+#SBATCH --output=$SCRATCH/logs/dynamate/dynamate_%j_%N.out
+#SBATCH --error=$SCRATCH/logs/dynamate/dynamate_%j_%N.err
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+#SBATCH --gpus-per-task=1
+#SBATCH --time=01:00:00
+#SBATCH --environment="/capstor/store/cscs/swissai/a131/bnaida/ce-images/dynamate/md_tools_v0.1.0.toml"
+
+set -e
+mkdir -p agent_logs
+
+PYTHON=/capstor/store/cscs/swissai/a131/bnaida/conda-envs/dynamate/bin/python
+cd /capstor/store/cscs/swissai/a131/$USER/projects/DynaMate
+
+CSV_FILE="Launch/systems.csv"
+FAILED_SYSTEMS="Launch/failed_systems.txt"
+
+if [[ ! -f "$CSV_FILE" ]]; then
+    echo "[ERROR] CSV file not found: $CSV_FILE"
+    exit 1
+fi
+
+NODE_ID=$SLURM_NODEID
+GPU_ID=$SLURM_LOCALID
+GPUS_PER_NODE=4
+
+TOTAL_ROWS=$(tail -n +2 "$CSV_FILE" | wc -l)
+DATA_PER_NODE=$(( TOTAL_ROWS / SLURM_NNODES ))
+DATA_PER_GPU=$(( DATA_PER_NODE / GPUS_PER_NODE ))
+
+START_ROW=$(( NODE_ID * DATA_PER_NODE + GPU_ID * DATA_PER_GPU ))
+END_ROW=$(( START_ROW + DATA_PER_GPU - 1 ))
+
+LINE_NUM=$((START_ROW - 1))
+tail -n +2 "$CSV_FILE" | tail -n +$START_ROW | head -n $DATA_PER_GPU \
+| while IFS=',' read -r PROTEIN LIGAND MODEL; do
+    ((LINE_NUM++))
+
+    echo "[INFO] Processing CSV line $LINE_NUM"
+
+    # Trim leading/trailing spaces
+    PROTEIN=$(echo "$PROTEIN" | xargs)
+    LIGAND=$(echo "$LIGAND" | xargs)
+    MODEL=$(echo "$MODEL" | xargs)
+    
+    # Take only the last part of the model name after the last '/'
+    MODEL_SHORT=${MODEL##*/}
+    echo "Model='$MODEL'"
+
+    # Handle missing ligand
+    if [[ "$LIGAND" == "" || "$LIGAND" == "None" || "$LIGAND" == "none" ]]; then
+        LIG_ARG="None"
+    else
+        LIG_ARG="$LIGAND"
+    fi
+
+    for RUN in 1 2 3; do
+        
+        LOGFILE="agent_logs/${PROTEIN}_${LIG_ARG}_${MODEL_SHORT}_run${RUN}.log"
+
+        echo "------------------------------------------------------"
+        echo "[INFO] Running: Protein=$PROTEIN | Ligand=$LIG_ARG | Model=$MODEL (Repeat $RUN/3)"
+        echo "[INFO] Output → $LOGFILE"
+        echo "------------------------------------------------------"
+
+        # Run the Python script
+        if ! $PYTHON -u main.py \
+            --pdb_id "$PROTEIN" \
+            --ligand "$LIG_ARG" \
+            --model "$MODEL" \
+            --temp 300 \
+            --duration 0.01 \
+            > "$LOGFILE" 2>&1
+        then
+            echo "[WARN] DynaMate failed for $PROTEIN $LIG_ARG, run $RUN."  | tee -a "$FAILED_SYSTEMS"
+        fi
+
+        echo "[INFO] Finished run $RUN for $PROTEIN ($MODEL)."
+
+    done
+
+    # Save progress
+    echo $((LINE_NUM + 1)) > "$CHECKPOINT"
+
+done
+
+echo "[INFO] All runs completed!"
diff --git a/Launch_scripts/systems.csv b/Launch_scripts/systems.csv
new file mode 100644
index 0000000..ab9ac79
--- /dev/null
+++ b/Launch_scripts/systems.csv
@@ -0,0 +1,992 @@
+entry_pdb_id,ligand_unique_ccd_code,model
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diff --git a/Launch_scripts/workstation_launch.sh b/Launch_scripts/workstation_launch.sh
new file mode 100755
index 0000000..8911ea0
--- /dev/null
+++ b/Launch_scripts/workstation_launch.sh
@@ -0,0 +1,76 @@
+#!/bin/bash
+
+echo "[INFO] Loading environment..."
+source setup.sh
+
+CSV_FILE="Launch/systems.csv"
+CHECKPOINT=".csv_checkpoint"
+FAILED_SYSTEMS="Launch/failed_systems.txt"
+
+if [[ ! -f "$CSV_FILE" ]]; then
+    echo "[ERROR] CSV file not found: $CSV_FILE"
+    exit 1
+fi
+
+echo "[INFO] Starting sequential execution..."
+echo "[INFO] Each system will be run 3 times."
+echo
+
+# Load starting line (default=2)
+START_LINE=2
+[[ -s "$CHECKPOINT" ]] && START_LINE=$(<"$CHECKPOINT")
+
+# Iterate through CSV (skip header)
+LINE_NUM=$((START_LINE - 1))
+tail -n +$START_LINE "$CSV_FILE" | while IFS=',' read -r PROTEIN LIGAND MODEL; do
+    ((LINE_NUM++))
+
+    echo "[INFO] Processing CSV line $LINE_NUM"
+
+    # Trim leading/trailing spaces
+    PROTEIN=$(echo "$PROTEIN" | xargs)
+    LIGAND=$(echo "$LIGAND" | xargs)
+    MODEL=$(echo "$MODEL" | xargs)
+    
+    # Take only the last part of the model name after the last '/'
+    MODEL_SHORT=${MODEL##*/}
+    echo "Model='$MODEL'"
+
+    # Handle missing ligand
+    if [[ "$LIGAND" == "" || "$LIGAND" == "None" || "$LIGAND" == "none" ]]; then
+        LIG_ARG="None"
+    else
+        LIG_ARG="$LIGAND"
+    fi
+
+    for RUN in 1 2 3; do
+        
+        LOGFILE="agent_logs/${PROTEIN}_${LIG_ARG}_${MODEL_SHORT}_run${RUN}.log"
+
+        echo "------------------------------------------------------"
+        echo "[INFO] Running: Protein=$PROTEIN | Ligand=$LIG_ARG | Model=$MODEL (Repeat $RUN/3)"
+        echo "[INFO] Output → $LOGFILE"
+        echo "------------------------------------------------------"
+
+        # Run the Python script
+        if ! python main.py \
+            --pdb_id "$PROTEIN" \
+            --ligand "$LIG_ARG" \
+            --model "$MODEL" \
+            --temp 300 \
+            --duration 0.01 \
+            > "$LOGFILE" 2>&1
+        then
+            echo "[WARN] DynaMate failed for $PROTEIN $LIG_ARG, run $RUN."  | tee -a "$FAILED_SYSTEMS"
+        fi
+
+        echo "[INFO] Finished run $RUN for $PROTEIN ($MODEL)."
+
+    done
+
+    # Save progress
+    echo $((LINE_NUM + 1)) > "$CHECKPOINT"
+
+done
+
+echo "[INFO] All runs completed!"
diff --git a/src/agents/md_agent.py b/src/agents/md_agent.py
index f388590..8a35b22 100644
--- a/src/agents/md_agent.py
+++ b/src/agents/md_agent.py
@@ -212,7 +212,7 @@ def _run_agent(self, remaining_steps: list[str]):
                 "Execute the molecular dynamics pipeline. The required steps are:\n"
                 f"{remaining_steps_string}\n\n"
                 "Work through each step in order using the available tools. "
-                "Ask the user if you need clarification on any step."
+                "Do not ask the user anything."
             ),
         })
 
@@ -223,7 +223,8 @@ def _run_agent(self, remaining_steps: list[str]):
 
             if iteration == MAX_ITERATIONS:
                 print(f"\n[Warning] Pipeline has reached {MAX_ITERATIONS} iterations without completing.")
-                answer = input("Would you like to quit and get a summary of what went wrong? (yes/no): ").strip().lower()
+                # answer = input("Would you like to quit and get a summary of what went wrong? (yes/no): ").strip().lower()
+                answer = "yes"
                 if answer in ("yes", "y"):
                     self.logger.info(f"User chose to quit after {iteration} iterations.")
                     return
@@ -244,7 +245,8 @@ def _run_agent(self, remaining_steps: list[str]):
                         print(f"\nAgent: {response.content}")
                     else:
                         print("\nAgent: I need your input to continue.")
-                    user_input = input("You: ").strip()
+                    # user_input = input("You: ").strip()
+                    user_input = "No input provided, please make your own decision to help the pipeline continue."
                     self.messages.append({"role": "user", "content": user_input})
 
             except Exception as e:
@@ -276,7 +278,8 @@ def _run_agent(self, remaining_steps: list[str]):
                     self.messages.append({"role": "assistant", "content": response.content})
                     if response.content:
                         print(f"\nAgent: {response.content}")
-                    user_input = input("You (press Enter to exit): ").strip()
+                    # user_input = input("You (press Enter to exit): ").strip()
+                    user_input = None
                     if not user_input:
                         self.logger.info("User exited post-pipeline conversation.")
                         break
diff --git a/src/agents/prep_agent.py b/src/agents/prep_agent.py
index 3df7aa0..af82bc2 100644
--- a/src/agents/prep_agent.py
+++ b/src/agents/prep_agent.py
@@ -141,7 +141,8 @@ def _get_pdb_file_path(self, prompt):
                 self.messages.append({"role": "assistant", "content": response.content})
                 if response.content:
                     print(f"\nAgent: {response.content}")
-                user_input = input("You: ").strip()
+                user_input = "No input provided, please make your own decision to help the pipeline continue."
+                # user_input = input("You: ").strip()
                 if user_input:
                     self.messages.append({"role": "user", "content": user_input})
 
@@ -162,10 +163,10 @@ def _find_ligand(self):
             lig_name = re.search(r"^[A-Z0-9]{3}$", user_input)
             if not lig_name:
                 self.logger.error(
-                    f"'{user_input}' is not a valid 3-character ligand code."
+                    f"'{user_input}' is not a valid 3-character ligand code. Continuing without a ligand."
                 )
-                self.ligand_name = input("Please enter the three character identifier for the ligand (or press Enter to skip): ").strip().upper() or None
-                continue
+                self.ligand_name = None
+                return
 
             self.ligand_name = lig_name.group()
             self.logger.info(f"User requested ligand: {self.ligand_name}")
@@ -183,7 +184,7 @@ def _find_ligand(self):
             self.logger.error(
                 f"Ligand '{self.ligand_name}' not found in {self.pdb_file_path}."
             )
-            self.ligand_name = input("Please enter the correct three character identifier for the ligand (or press Enter to skip): ").strip().upper() or None
+            self.ligand_name = None
 
     def _find_simulation_temperature(self):
         temperature = self.md_temp

From 2579ed86a379ea19de3a0dc6f7452516423b0d12 Mon Sep 17 00:00:00 2001
From: Cassandra Masschelein <cassandra@clariden-ln003.cscs.ch>
Date: Fri, 8 May 2026 13:26:39 +0200
Subject: [PATCH 02/14] remove checkpoint tracking

---
 Launch_scripts/cscs_launch.sh | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/Launch_scripts/cscs_launch.sh b/Launch_scripts/cscs_launch.sh
index 5edd63f..d86fff5 100644
--- a/Launch_scripts/cscs_launch.sh
+++ b/Launch_scripts/cscs_launch.sh
@@ -2,8 +2,8 @@
 #SBATCH --account=a131
 #SBATCH --partition=debug
 #SBATCH --job-name=dynamate
-#SBATCH --output=$SCRATCH/logs/dynamate/dynamate_%j_%N.out
-#SBATCH --error=$SCRATCH/logs/dynamate/dynamate_%j_%N.err
+#SBATCH --output=slurm_logs/launch_%j_%N.out
+#SBATCH --error=slurm_logs/launch_%j_%N.err
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=4
 #SBATCH --gpus-per-task=1
@@ -11,10 +11,10 @@
 #SBATCH --environment="/capstor/store/cscs/swissai/a131/bnaida/ce-images/dynamate/md_tools_v0.1.0.toml"
 
 set -e
-mkdir -p agent_logs
+mkdir -p agent_logs slurm_logs
 
 PYTHON=/capstor/store/cscs/swissai/a131/bnaida/conda-envs/dynamate/bin/python
-cd /capstor/store/cscs/swissai/a131/$USER/projects/DynaMate
+cd /capstor/store/cscs/swissai/a131/cassandra/projects/DynaMate
 
 CSV_FILE="Launch/systems.csv"
 FAILED_SYSTEMS="Launch/failed_systems.txt"
@@ -66,7 +66,6 @@ tail -n +2 "$CSV_FILE" | tail -n +$START_ROW | head -n $DATA_PER_GPU \
         echo "[INFO] Running: Protein=$PROTEIN | Ligand=$LIG_ARG | Model=$MODEL (Repeat $RUN/3)"
         echo "[INFO] Output → $LOGFILE"
         echo "------------------------------------------------------"
-
         # Run the Python script
         if ! $PYTHON -u main.py \
             --pdb_id "$PROTEIN" \
@@ -78,14 +77,8 @@ tail -n +2 "$CSV_FILE" | tail -n +$START_ROW | head -n $DATA_PER_GPU \
         then
             echo "[WARN] DynaMate failed for $PROTEIN $LIG_ARG, run $RUN."  | tee -a "$FAILED_SYSTEMS"
         fi
-
         echo "[INFO] Finished run $RUN for $PROTEIN ($MODEL)."
-
     done
-
-    # Save progress
-    echo $((LINE_NUM + 1)) > "$CHECKPOINT"
-
 done
 
 echo "[INFO] All runs completed!"

From 7b3cacc559191b9c36d3214eaf4f55dc7fbbb0b3 Mon Sep 17 00:00:00 2001
From: Cassandra Masschelein <cassandra@clariden-ln003.cscs.ch>
Date: Fri, 8 May 2026 13:35:42 +0200
Subject: [PATCH 03/14] fixed log files

---
 Launch_scripts/cscs_launch.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/Launch_scripts/cscs_launch.sh b/Launch_scripts/cscs_launch.sh
index d86fff5..9c83d5a 100644
--- a/Launch_scripts/cscs_launch.sh
+++ b/Launch_scripts/cscs_launch.sh
@@ -11,13 +11,14 @@
 #SBATCH --environment="/capstor/store/cscs/swissai/a131/bnaida/ce-images/dynamate/md_tools_v0.1.0.toml"
 
 set -e
-mkdir -p agent_logs slurm_logs
 
 PYTHON=/capstor/store/cscs/swissai/a131/bnaida/conda-envs/dynamate/bin/python
 cd /capstor/store/cscs/swissai/a131/cassandra/projects/DynaMate
 
-CSV_FILE="Launch/systems.csv"
-FAILED_SYSTEMS="Launch/failed_systems.txt"
+mkdir -p agent_logs slurm_logs
+
+CSV_FILE="Launch_scripts/systems.csv"
+FAILED_SYSTEMS="Launch_scripts/failed_systems.txt"
 
 if [[ ! -f "$CSV_FILE" ]]; then
     echo "[ERROR] CSV file not found: $CSV_FILE"

From 9c8584de3568ccaf8c0d711736c426811200ed1a Mon Sep 17 00:00:00 2001
From: Cassandra Masschelein <cassandramasschelein@gmail.com>
Date: Mon, 11 May 2026 13:30:14 +0200
Subject: [PATCH 04/14] update launch scripts

---
 Launch_scripts/cscs_launch.sh | 12 ++++++-
 Launch_scripts/new_launch.sh  | 32 ++++++++++++++++++
 Launch_scripts/systems.csv    |  1 -
 Launch_scripts/worker.sh      | 64 +++++++++++++++++++++++++++++++++++
 4 files changed, 107 insertions(+), 2 deletions(-)
 create mode 100644 Launch_scripts/new_launch.sh
 create mode 100644 Launch_scripts/worker.sh

diff --git a/Launch_scripts/cscs_launch.sh b/Launch_scripts/cscs_launch.sh
index 9c83d5a..275a588 100644
--- a/Launch_scripts/cscs_launch.sh
+++ b/Launch_scripts/cscs_launch.sh
@@ -7,9 +7,14 @@
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=4
 #SBATCH --gpus-per-task=1
-#SBATCH --time=01:00:00
+#SBATCH --time=00:10:00
 #SBATCH --environment="/capstor/store/cscs/swissai/a131/bnaida/ce-images/dynamate/md_tools_v0.1.0.toml"
 
+# srun ./testing.sh
+
+
+# slurm_procid
+
 set -e
 
 PYTHON=/capstor/store/cscs/swissai/a131/bnaida/conda-envs/dynamate/bin/python
@@ -20,6 +25,8 @@ mkdir -p agent_logs slurm_logs
 CSV_FILE="Launch_scripts/systems.csv"
 FAILED_SYSTEMS="Launch_scripts/failed_systems.txt"
 
+echo "sees GPUs: $CUDA_VISIBLE_DEVICES"
+
 if [[ ! -f "$CSV_FILE" ]]; then
     echo "[ERROR] CSV file not found: $CSV_FILE"
     exit 1
@@ -42,6 +49,7 @@ tail -n +2 "$CSV_FILE" | tail -n +$START_ROW | head -n $DATA_PER_GPU \
     ((LINE_NUM++))
 
     echo "[INFO] Processing CSV line $LINE_NUM"
+    echo "Made it into the first GPU"
 
     # Trim leading/trailing spaces
     PROTEIN=$(echo "$PROTEIN" | xargs)
@@ -60,6 +68,7 @@ tail -n +2 "$CSV_FILE" | tail -n +$START_ROW | head -n $DATA_PER_GPU \
     fi
 
     for RUN in 1 2 3; do
+        echo "[INFO] Starting run $RUN for $PROTEIN ($MODEL)."
         
         LOGFILE="agent_logs/${PROTEIN}_${LIG_ARG}_${MODEL_SHORT}_run${RUN}.log"
 
@@ -67,6 +76,7 @@ tail -n +2 "$CSV_FILE" | tail -n +$START_ROW | head -n $DATA_PER_GPU \
         echo "[INFO] Running: Protein=$PROTEIN | Ligand=$LIG_ARG | Model=$MODEL (Repeat $RUN/3)"
         echo "[INFO] Output → $LOGFILE"
         echo "------------------------------------------------------"
+        echo "about to enter the main.py script!"
         # Run the Python script
         if ! $PYTHON -u main.py \
             --pdb_id "$PROTEIN" \
diff --git a/Launch_scripts/new_launch.sh b/Launch_scripts/new_launch.sh
new file mode 100644
index 0000000..d07b17f
--- /dev/null
+++ b/Launch_scripts/new_launch.sh
@@ -0,0 +1,32 @@
+#!/bin/bash
+#SBATCH --account=a131
+#SBATCH --partition=debug
+#SBATCH --job-name=dynamate_launch
+#SBATCH --output=slurm_logs/launch_%j_%N.out
+#SBATCH --error=slurm_logs/launch_%j_%N.err
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+#SBATCH --gpus-per-task=1
+#SBATCH --time=00:10:00
+
+set -e
+
+mkdir -p agent_logs slurm_logs
+
+# --- Exported config inherited by all worker tasks ---
+export PYTHON=/capstor/store/cscs/swissai/a131/bnaida/conda-envs/dynamate/bin/python
+export WORK_DIR=/capstor/store/cscs/swissai/a131/cassandra/projects/DynaMate
+export CSV_FILE="Launch_scripts/systems.csv"
+export FAILED_SYSTEMS="Launch_scripts/failed_systems.txt"
+export GPUS_PER_NODE=4
+
+cd $WORK_DIR
+
+if [[ ! -f "$CSV_FILE" ]]; then
+    echo "[ERROR] CSV file not found: $CSV_FILE"
+    exit 1
+fi
+
+srun --ntasks=4 --ntasks-per-node=4 --gpus-per-task=1 \
+    --environment="/capstor/store/cscs/swissai/a131/bnaida/ce-images/dynamate/md_tools_v0.1.0.toml" \
+    bash /capstor/store/cscs/swissai/a131/cassandra/projects/DynaMate/Launch_scripts/worker.sh
diff --git a/Launch_scripts/systems.csv b/Launch_scripts/systems.csv
index ab9ac79..f93456b 100644
--- a/Launch_scripts/systems.csv
+++ b/Launch_scripts/systems.csv
@@ -1,5 +1,4 @@
 entry_pdb_id,ligand_unique_ccd_code,model
-7grs,NT9,openrouter/openai/gpt-5-mini
 1dy4,SNP,openrouter/openai/gpt-5-mini
 7a4q,QY2,openrouter/openai/gpt-5-mini
 4a4q,UX9,openrouter/openai/gpt-5-mini
diff --git a/Launch_scripts/worker.sh b/Launch_scripts/worker.sh
new file mode 100644
index 0000000..d9113bd
--- /dev/null
+++ b/Launch_scripts/worker.sh
@@ -0,0 +1,64 @@
+#!/bin/bash
+# worker.sh — executed once per srun task
+#
+# SLURM variables set per-task:
+#   $SLURM_NODEID    — node index (0..NODES-1)
+#   $SLURM_LOCALID   — local GPU rank on this node (0..GPUS_PER_NODE-1)
+#   $SLURM_NNODES    — total number of nodes
+#
+# Inherited from submit.sh:
+#   $PYTHON, $WORK_DIR, $CSV_FILE, $FAILED_SYSTEMS, $GPUS_PER_NODE
+
+cd $WORK_DIR
+
+NODE_ID=$SLURM_NODEID
+GPU_ID=$SLURM_LOCALID   # 0-indexed within the node
+
+echo "[INFO] Node $NODE_ID | GPU $GPU_ID | sees CUDA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES"
+
+# --- Chunk the CSV across nodes and GPUs ---
+TOTAL_ROWS=$(tail -n +2 "$CSV_FILE" | wc -l)
+DATA_PER_NODE=$(( TOTAL_ROWS / SLURM_NNODES ))
+DATA_PER_GPU=$(( DATA_PER_NODE / GPUS_PER_NODE ))
+
+START_ROW=$(( NODE_ID * DATA_PER_NODE + GPU_ID * DATA_PER_GPU + 1 ))  # +1: tail is 1-indexed
+
+echo "[INFO] Handling rows $START_ROW to $(( START_ROW + DATA_PER_GPU - 1 )) of $TOTAL_ROWS"
+
+tail -n +2 "$CSV_FILE" | tail -n +"$START_ROW" | head -n "$DATA_PER_GPU" \
+| while IFS=',' read -r PROTEIN LIGAND MODEL; do
+
+    PROTEIN=$(echo "$PROTEIN" | xargs)
+    LIGAND=$(echo "$LIGAND"   | xargs)
+    MODEL=$(echo "$MODEL"     | xargs)
+    MODEL_SHORT=${MODEL##*/}
+
+    LIG_ARG="None"
+    if [[ -n "$LIGAND" && "$LIGAND" != "None" && "$LIGAND" != "none" ]]; then
+        LIG_ARG="$LIGAND"
+    fi
+
+    for RUN in 1 2 3; do
+        LOGFILE="agent_logs/${PROTEIN}_${LIG_ARG}_${MODEL_SHORT}_run${RUN}.log"
+
+        echo "------------------------------------------------------"
+        echo "[INFO] Node=$NODE_ID GPU=$GPU_ID | $PROTEIN | $LIG_ARG | $MODEL_SHORT | Run $RUN/3"
+        echo "[INFO] Output → $LOGFILE"
+        echo "------------------------------------------------------"
+
+        if ! $PYTHON -u main.py \
+            --pdb_id  "$PROTEIN" \
+            --ligand  "$LIG_ARG" \
+            --model   "$MODEL" \
+            --temp    300 \
+            --duration 0.01 \
+            > "$LOGFILE" 2>&1
+        then
+            echo "[WARN] Failed: $PROTEIN $LIG_ARG run $RUN" | tee -a "$FAILED_SYSTEMS"
+        fi
+
+        echo "[INFO] Finished run $RUN for $PROTEIN ($MODEL_SHORT)."
+    done
+done
+
+echo "[INFO] Node $NODE_ID | GPU $GPU_ID | All rows complete."
\ No newline at end of file

From 9a274d71a3e37f5b19ca175110ac9a5ac88b61e5 Mon Sep 17 00:00:00 2001
From: cassandra <cassandramasschelein@gmail.com>
Date: Mon, 11 May 2026 14:54:28 +0200
Subject: [PATCH 05/14] filter systems for launch + bug fix

---
 Launch_scripts/plinder_job_filter.ipynb      |  52 +++
 Launch_scripts/plinder_launch_complete.csv   | 335 ++++++++++++++++++
 Launch_scripts/plinder_launch_incomplete.csv | 346 +++++++++++++++++++
 src/agents/agent.py                          |  11 +-
 src/tools/pdb_tools.py                       |   5 +-
 5 files changed, 745 insertions(+), 4 deletions(-)
 create mode 100644 Launch_scripts/plinder_job_filter.ipynb
 create mode 100644 Launch_scripts/plinder_launch_complete.csv
 create mode 100644 Launch_scripts/plinder_launch_incomplete.csv

diff --git a/Launch_scripts/plinder_job_filter.ipynb b/Launch_scripts/plinder_job_filter.ipynb
new file mode 100644
index 0000000..c53d99a
--- /dev/null
+++ b/Launch_scripts/plinder_job_filter.ipynb
@@ -0,0 +1,52 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "\n",
+    "df_incomplete = pd.read_csv('plinder_launch_incomplete.csv')\n",
+    "\n",
+    "# 165 randomly selected protein-ligand systems\n",
+    "protein_ligand = df_incomplete.sample(n=165, random_state=42).reset_index(drop=True)\n",
+    "\n",
+    "# 100 randomly selected protein-only systems (ligand code blank)\n",
+    "protein_only = df_incomplete.sample(n=100, random_state=7).reset_index(drop=True)\n",
+    "protein_only['ligand_unique_ccd_code'] = ''\n",
+    "\n",
+    "combined = pd.concat([protein_ligand, protein_only], ignore_index=True)\n",
+    "\n",
+    "print(f'Total systems: {len(combined)}')\n",
+    "print(f'Protein-ligand: {len(protein_ligand)}')\n",
+    "print(f'Protein-only:   {len(protein_only)}')\n",
+    "combined.head(10)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "combined.to_csv('plinder_job_filter_output.csv', index=False)\n",
+    "print('Saved to plinder_job_filter_output.csv')"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "dynamate_data",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/Launch_scripts/plinder_launch_complete.csv b/Launch_scripts/plinder_launch_complete.csv
new file mode 100644
index 0000000..70608f0
--- /dev/null
+++ b/Launch_scripts/plinder_launch_complete.csv
@@ -0,0 +1,335 @@
+entry_pdb_id,ligand_unique_ccd_code,model
+4hj3,FMN,openrouter/openai/gpt-5-mini
+7m8r,W6X,openrouter/openai/gpt-5-mini
+5jg5,EVF,openrouter/openai/gpt-5-mini
+6dh1,K13,openrouter/openai/gpt-5-mini
+4j2a,TTP,openrouter/openai/gpt-5-mini
+1fm6,BRL,openrouter/openai/gpt-5-mini
+4ufx,NHW,openrouter/openai/gpt-5-mini
+6tx7,V1L,openrouter/openai/gpt-5-mini
+4tta,FMC,openrouter/openai/gpt-5-mini
+1wuw,SEG,openrouter/openai/gpt-5-mini
+6dws,HFY,openrouter/openai/gpt-5-mini
+7qzz,HHT,openrouter/openai/gpt-5-mini
+6f57,SAH,openrouter/openai/gpt-5-mini
+3qls,GLY,openrouter/openai/gpt-5-mini
+3s9h,DUP,openrouter/openai/gpt-5-mini
+3l72,IKR,openrouter/openai/gpt-5-mini
+5e9i,F60,openrouter/openai/gpt-5-mini
+4xn4,MET,openrouter/openai/gpt-5-mini
+5c4s,4Y5,openrouter/openai/gpt-5-mini
+6opv,017,openrouter/openai/gpt-5-mini
+5x1f,CHD,openrouter/openai/gpt-5-mini
+5ytd,DGT,openrouter/openai/gpt-5-mini
+2w26,RIV,openrouter/openai/gpt-5-mini
+3qlh,MNK,openrouter/openai/gpt-5-mini
+4tti,FMC,openrouter/openai/gpt-5-mini
+1bxh,MMA,openrouter/openai/gpt-5-mini
+6dh0,017,openrouter/openai/gpt-5-mini
+4xo4,MET,openrouter/openai/gpt-5-mini
+1jof,PIN,openrouter/openai/gpt-5-mini
+8c6o,CZH,openrouter/openai/gpt-5-mini
+3oy4,017,openrouter/openai/gpt-5-mini
+7a4q,QY2,openrouter/openai/gpt-5-mini
+7ma1,065,openrouter/openai/gpt-5-mini
+8jea,MAN,openrouter/openai/gpt-5-mini
+4zsg,4QX,openrouter/openai/gpt-5-mini
+4xmz,DAB,openrouter/openai/gpt-5-mini
+4l1e,BLA,openrouter/openai/gpt-5-mini
+7ma4,K2A,openrouter/openai/gpt-5-mini
+7ma3,K14,openrouter/openai/gpt-5-mini
+1tke,SEG,openrouter/openai/gpt-5-mini
+3iai,AZM,openrouter/openai/gpt-5-mini
+3sq4,TTP,openrouter/openai/gpt-5-mini
+6g2r,EJK,openrouter/openai/gpt-5-mini
+7vm6,7R8,openrouter/openai/gpt-5-mini
+3nu9,478,openrouter/openai/gpt-5-mini
+3qsy,GNP,openrouter/openai/gpt-5-mini
+5jgs,EVF,openrouter/openai/gpt-5-mini
+3ma0,HSZ,openrouter/openai/gpt-5-mini
+3ar2,ACP,openrouter/openai/gpt-5-mini
+2onj,ANP,openrouter/openai/gpt-5-mini
+7u31,L7I,openrouter/openai/gpt-5-mini
+6c7d,EOJ,openrouter/openai/gpt-5-mini
+6q60,HJH,openrouter/openai/gpt-5-mini
+5hnu,NAP,openrouter/openai/gpt-5-mini
+3cic,316,openrouter/openai/gpt-5-mini
+2x96,RX3,openrouter/openai/gpt-5-mini
+7ve7,NAP,openrouter/openai/gpt-5-mini
+1bxh,MAM,openrouter/openai/gpt-5-mini
+3llm,ADP,openrouter/openai/gpt-5-mini
+3gi4,K60,openrouter/openai/gpt-5-mini
+1fl3,SPB,openrouter/openai/gpt-5-mini
+4xob,KGM,openrouter/openai/gpt-5-mini
+4e5p,NAD,openrouter/openai/gpt-5-mini
+3qp8,HL0,openrouter/openai/gpt-5-mini
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diff --git a/Launch_scripts/plinder_launch_incomplete.csv b/Launch_scripts/plinder_launch_incomplete.csv
new file mode 100644
index 0000000..06a9859
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diff --git a/src/agents/agent.py b/src/agents/agent.py
index 45ec8e5..56bb5de 100644
--- a/src/agents/agent.py
+++ b/src/agents/agent.py
@@ -1,4 +1,5 @@
 import os
+import time
 from pathlib import Path
 from typing import Dict, Any, List
 import json
@@ -177,15 +178,19 @@ def _safe_execute_tool(self, tool_name: str, tool_input: Dict[str, Any]) -> dict
                 self.logger.error(error_msg)
                 return {"ok": False, "output": error_msg}
 
-        tool_output = None
-
         self._validate_tool_path(tool_input)
         func = TOOL_MAP.get(tool_name)
 
         if not func:
             raise ValueError(f"Unknown tool: {tool_name}")
 
-        tool_output = func(self, tool_input)
+        try:
+            tool_output = func(self, tool_input)
+        except Exception as e:
+            error_msg = f"Tool '{tool_name}' raised an exception: {type(e).__name__}: {e}\n{traceback.format_exc()}"
+            self.logger.error(error_msg)
+            return {"ok": False, "output": error_msg}
+
         passed = self._additional_check_for_errors_tool_output(tool_name, tool_output)
 
         return {"ok": passed, "output": tool_output}
diff --git a/src/tools/pdb_tools.py b/src/tools/pdb_tools.py
index 38c4ba0..c433c7d 100644
--- a/src/tools/pdb_tools.py
+++ b/src/tools/pdb_tools.py
@@ -208,7 +208,10 @@ def prepare_pdb_file_ligand(sandbox_dir: str, pdb_id: str, ligand_name: str = No
                 list_protonated_files.append(f"{ligand_name}_{index}_h.pdb")
             
             cmd = shlex.split(f"obabel {ligand_pdb_file} -O {protonated_file} -p7")
-            subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            if result.returncode != 0 or not os.path.exists(protonated_file):
+                error_detail = result.stderr.decode(errors="replace").strip() or result.stdout.decode(errors="replace").strip()
+                return f"obabel failed to protonate {ligand_pdb_file} (return code {result.returncode}): {error_detail}"
             with open(protonated_file, "r") as infile:
                 lines = infile.readlines()
                 filtered_lines = [line for line in lines if not (line.startswith("CONECT") or line.startswith("MASTER"))]

From 6f2f6a5e45f2d70e53f5a242e47fd8443ae8242f Mon Sep 17 00:00:00 2001
From: Cassandra Masschelein <cassandramasschelein@gmail.com>
Date: Mon, 11 May 2026 16:23:10 +0200
Subject: [PATCH 06/14] stop tracking launch scripts, add to gitignore

---
 .gitignore                                   |   1 +
 Launch_scripts/cscs_launch.sh                |  95 --
 Launch_scripts/new_launch.sh                 |  32 -
 Launch_scripts/plinder_job_filter.ipynb      |  52 -
 Launch_scripts/plinder_launch_complete.csv   | 335 -------
 Launch_scripts/plinder_launch_incomplete.csv | 346 -------
 Launch_scripts/systems.csv                   | 991 -------------------
 Launch_scripts/worker.sh                     |  64 --
 Launch_scripts/workstation_launch.sh         |  76 --
 9 files changed, 1 insertion(+), 1991 deletions(-)
 delete mode 100644 Launch_scripts/cscs_launch.sh
 delete mode 100644 Launch_scripts/new_launch.sh
 delete mode 100644 Launch_scripts/plinder_job_filter.ipynb
 delete mode 100644 Launch_scripts/plinder_launch_complete.csv
 delete mode 100644 Launch_scripts/plinder_launch_incomplete.csv
 delete mode 100644 Launch_scripts/systems.csv
 delete mode 100644 Launch_scripts/worker.sh
 delete mode 100755 Launch_scripts/workstation_launch.sh

diff --git a/.gitignore b/.gitignore
index 8f50ecd..71ee47a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -30,3 +30,4 @@ software/
 Launch/
 Plotting/
 extra_logs/
+Launch_scripts/
diff --git a/Launch_scripts/cscs_launch.sh b/Launch_scripts/cscs_launch.sh
deleted file mode 100644
index 275a588..0000000
--- a/Launch_scripts/cscs_launch.sh
+++ /dev/null
@@ -1,95 +0,0 @@
-#!/bin/bash
-#SBATCH --account=a131
-#SBATCH --partition=debug
-#SBATCH --job-name=dynamate
-#SBATCH --output=slurm_logs/launch_%j_%N.out
-#SBATCH --error=slurm_logs/launch_%j_%N.err
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=4
-#SBATCH --gpus-per-task=1
-#SBATCH --time=00:10:00
-#SBATCH --environment="/capstor/store/cscs/swissai/a131/bnaida/ce-images/dynamate/md_tools_v0.1.0.toml"
-
-# srun ./testing.sh
-
-
-# slurm_procid
-
-set -e
-
-PYTHON=/capstor/store/cscs/swissai/a131/bnaida/conda-envs/dynamate/bin/python
-cd /capstor/store/cscs/swissai/a131/cassandra/projects/DynaMate
-
-mkdir -p agent_logs slurm_logs
-
-CSV_FILE="Launch_scripts/systems.csv"
-FAILED_SYSTEMS="Launch_scripts/failed_systems.txt"
-
-echo "sees GPUs: $CUDA_VISIBLE_DEVICES"
-
-if [[ ! -f "$CSV_FILE" ]]; then
-    echo "[ERROR] CSV file not found: $CSV_FILE"
-    exit 1
-fi
-
-NODE_ID=$SLURM_NODEID
-GPU_ID=$SLURM_LOCALID
-GPUS_PER_NODE=4
-
-TOTAL_ROWS=$(tail -n +2 "$CSV_FILE" | wc -l)
-DATA_PER_NODE=$(( TOTAL_ROWS / SLURM_NNODES ))
-DATA_PER_GPU=$(( DATA_PER_NODE / GPUS_PER_NODE ))
-
-START_ROW=$(( NODE_ID * DATA_PER_NODE + GPU_ID * DATA_PER_GPU ))
-END_ROW=$(( START_ROW + DATA_PER_GPU - 1 ))
-
-LINE_NUM=$((START_ROW - 1))
-tail -n +2 "$CSV_FILE" | tail -n +$START_ROW | head -n $DATA_PER_GPU \
-| while IFS=',' read -r PROTEIN LIGAND MODEL; do
-    ((LINE_NUM++))
-
-    echo "[INFO] Processing CSV line $LINE_NUM"
-    echo "Made it into the first GPU"
-
-    # Trim leading/trailing spaces
-    PROTEIN=$(echo "$PROTEIN" | xargs)
-    LIGAND=$(echo "$LIGAND" | xargs)
-    MODEL=$(echo "$MODEL" | xargs)
-    
-    # Take only the last part of the model name after the last '/'
-    MODEL_SHORT=${MODEL##*/}
-    echo "Model='$MODEL'"
-
-    # Handle missing ligand
-    if [[ "$LIGAND" == "" || "$LIGAND" == "None" || "$LIGAND" == "none" ]]; then
-        LIG_ARG="None"
-    else
-        LIG_ARG="$LIGAND"
-    fi
-
-    for RUN in 1 2 3; do
-        echo "[INFO] Starting run $RUN for $PROTEIN ($MODEL)."
-        
-        LOGFILE="agent_logs/${PROTEIN}_${LIG_ARG}_${MODEL_SHORT}_run${RUN}.log"
-
-        echo "------------------------------------------------------"
-        echo "[INFO] Running: Protein=$PROTEIN | Ligand=$LIG_ARG | Model=$MODEL (Repeat $RUN/3)"
-        echo "[INFO] Output → $LOGFILE"
-        echo "------------------------------------------------------"
-        echo "about to enter the main.py script!"
-        # Run the Python script
-        if ! $PYTHON -u main.py \
-            --pdb_id "$PROTEIN" \
-            --ligand "$LIG_ARG" \
-            --model "$MODEL" \
-            --temp 300 \
-            --duration 0.01 \
-            > "$LOGFILE" 2>&1
-        then
-            echo "[WARN] DynaMate failed for $PROTEIN $LIG_ARG, run $RUN."  | tee -a "$FAILED_SYSTEMS"
-        fi
-        echo "[INFO] Finished run $RUN for $PROTEIN ($MODEL)."
-    done
-done
-
-echo "[INFO] All runs completed!"
diff --git a/Launch_scripts/new_launch.sh b/Launch_scripts/new_launch.sh
deleted file mode 100644
index d07b17f..0000000
--- a/Launch_scripts/new_launch.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/bin/bash
-#SBATCH --account=a131
-#SBATCH --partition=debug
-#SBATCH --job-name=dynamate_launch
-#SBATCH --output=slurm_logs/launch_%j_%N.out
-#SBATCH --error=slurm_logs/launch_%j_%N.err
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=4
-#SBATCH --gpus-per-task=1
-#SBATCH --time=00:10:00
-
-set -e
-
-mkdir -p agent_logs slurm_logs
-
-# --- Exported config inherited by all worker tasks ---
-export PYTHON=/capstor/store/cscs/swissai/a131/bnaida/conda-envs/dynamate/bin/python
-export WORK_DIR=/capstor/store/cscs/swissai/a131/cassandra/projects/DynaMate
-export CSV_FILE="Launch_scripts/systems.csv"
-export FAILED_SYSTEMS="Launch_scripts/failed_systems.txt"
-export GPUS_PER_NODE=4
-
-cd $WORK_DIR
-
-if [[ ! -f "$CSV_FILE" ]]; then
-    echo "[ERROR] CSV file not found: $CSV_FILE"
-    exit 1
-fi
-
-srun --ntasks=4 --ntasks-per-node=4 --gpus-per-task=1 \
-    --environment="/capstor/store/cscs/swissai/a131/bnaida/ce-images/dynamate/md_tools_v0.1.0.toml" \
-    bash /capstor/store/cscs/swissai/a131/cassandra/projects/DynaMate/Launch_scripts/worker.sh
diff --git a/Launch_scripts/plinder_job_filter.ipynb b/Launch_scripts/plinder_job_filter.ipynb
deleted file mode 100644
index c53d99a..0000000
--- a/Launch_scripts/plinder_job_filter.ipynb
+++ /dev/null
@@ -1,52 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import pandas as pd\n",
-    "\n",
-    "df_incomplete = pd.read_csv('plinder_launch_incomplete.csv')\n",
-    "\n",
-    "# 165 randomly selected protein-ligand systems\n",
-    "protein_ligand = df_incomplete.sample(n=165, random_state=42).reset_index(drop=True)\n",
-    "\n",
-    "# 100 randomly selected protein-only systems (ligand code blank)\n",
-    "protein_only = df_incomplete.sample(n=100, random_state=7).reset_index(drop=True)\n",
-    "protein_only['ligand_unique_ccd_code'] = ''\n",
-    "\n",
-    "combined = pd.concat([protein_ligand, protein_only], ignore_index=True)\n",
-    "\n",
-    "print(f'Total systems: {len(combined)}')\n",
-    "print(f'Protein-ligand: {len(protein_ligand)}')\n",
-    "print(f'Protein-only:   {len(protein_only)}')\n",
-    "combined.head(10)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "combined.to_csv('plinder_job_filter_output.csv', index=False)\n",
-    "print('Saved to plinder_job_filter_output.csv')"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "dynamate_data",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "name": "python",
-   "version": "3.10.12"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/Launch_scripts/plinder_launch_complete.csv b/Launch_scripts/plinder_launch_complete.csv
deleted file mode 100644
index 70608f0..0000000
--- a/Launch_scripts/plinder_launch_complete.csv
+++ /dev/null
@@ -1,335 +0,0 @@
-entry_pdb_id,ligand_unique_ccd_code,model
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diff --git a/Launch_scripts/plinder_launch_incomplete.csv b/Launch_scripts/plinder_launch_incomplete.csv
deleted file mode 100644
index 06a9859..0000000
--- a/Launch_scripts/plinder_launch_incomplete.csv
+++ /dev/null
@@ -1,346 +0,0 @@
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diff --git a/Launch_scripts/systems.csv b/Launch_scripts/systems.csv
deleted file mode 100644
index f93456b..0000000
--- a/Launch_scripts/systems.csv
+++ /dev/null
@@ -1,991 +0,0 @@
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diff --git a/Launch_scripts/worker.sh b/Launch_scripts/worker.sh
deleted file mode 100644
index d9113bd..0000000
--- a/Launch_scripts/worker.sh
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/bin/bash
-# worker.sh — executed once per srun task
-#
-# SLURM variables set per-task:
-#   $SLURM_NODEID    — node index (0..NODES-1)
-#   $SLURM_LOCALID   — local GPU rank on this node (0..GPUS_PER_NODE-1)
-#   $SLURM_NNODES    — total number of nodes
-#
-# Inherited from submit.sh:
-#   $PYTHON, $WORK_DIR, $CSV_FILE, $FAILED_SYSTEMS, $GPUS_PER_NODE
-
-cd $WORK_DIR
-
-NODE_ID=$SLURM_NODEID
-GPU_ID=$SLURM_LOCALID   # 0-indexed within the node
-
-echo "[INFO] Node $NODE_ID | GPU $GPU_ID | sees CUDA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES"
-
-# --- Chunk the CSV across nodes and GPUs ---
-TOTAL_ROWS=$(tail -n +2 "$CSV_FILE" | wc -l)
-DATA_PER_NODE=$(( TOTAL_ROWS / SLURM_NNODES ))
-DATA_PER_GPU=$(( DATA_PER_NODE / GPUS_PER_NODE ))
-
-START_ROW=$(( NODE_ID * DATA_PER_NODE + GPU_ID * DATA_PER_GPU + 1 ))  # +1: tail is 1-indexed
-
-echo "[INFO] Handling rows $START_ROW to $(( START_ROW + DATA_PER_GPU - 1 )) of $TOTAL_ROWS"
-
-tail -n +2 "$CSV_FILE" | tail -n +"$START_ROW" | head -n "$DATA_PER_GPU" \
-| while IFS=',' read -r PROTEIN LIGAND MODEL; do
-
-    PROTEIN=$(echo "$PROTEIN" | xargs)
-    LIGAND=$(echo "$LIGAND"   | xargs)
-    MODEL=$(echo "$MODEL"     | xargs)
-    MODEL_SHORT=${MODEL##*/}
-
-    LIG_ARG="None"
-    if [[ -n "$LIGAND" && "$LIGAND" != "None" && "$LIGAND" != "none" ]]; then
-        LIG_ARG="$LIGAND"
-    fi
-
-    for RUN in 1 2 3; do
-        LOGFILE="agent_logs/${PROTEIN}_${LIG_ARG}_${MODEL_SHORT}_run${RUN}.log"
-
-        echo "------------------------------------------------------"
-        echo "[INFO] Node=$NODE_ID GPU=$GPU_ID | $PROTEIN | $LIG_ARG | $MODEL_SHORT | Run $RUN/3"
-        echo "[INFO] Output → $LOGFILE"
-        echo "------------------------------------------------------"
-
-        if ! $PYTHON -u main.py \
-            --pdb_id  "$PROTEIN" \
-            --ligand  "$LIG_ARG" \
-            --model   "$MODEL" \
-            --temp    300 \
-            --duration 0.01 \
-            > "$LOGFILE" 2>&1
-        then
-            echo "[WARN] Failed: $PROTEIN $LIG_ARG run $RUN" | tee -a "$FAILED_SYSTEMS"
-        fi
-
-        echo "[INFO] Finished run $RUN for $PROTEIN ($MODEL_SHORT)."
-    done
-done
-
-echo "[INFO] Node $NODE_ID | GPU $GPU_ID | All rows complete."
\ No newline at end of file
diff --git a/Launch_scripts/workstation_launch.sh b/Launch_scripts/workstation_launch.sh
deleted file mode 100755
index 8911ea0..0000000
--- a/Launch_scripts/workstation_launch.sh
+++ /dev/null
@@ -1,76 +0,0 @@
-#!/bin/bash
-
-echo "[INFO] Loading environment..."
-source setup.sh
-
-CSV_FILE="Launch/systems.csv"
-CHECKPOINT=".csv_checkpoint"
-FAILED_SYSTEMS="Launch/failed_systems.txt"
-
-if [[ ! -f "$CSV_FILE" ]]; then
-    echo "[ERROR] CSV file not found: $CSV_FILE"
-    exit 1
-fi
-
-echo "[INFO] Starting sequential execution..."
-echo "[INFO] Each system will be run 3 times."
-echo
-
-# Load starting line (default=2)
-START_LINE=2
-[[ -s "$CHECKPOINT" ]] && START_LINE=$(<"$CHECKPOINT")
-
-# Iterate through CSV (skip header)
-LINE_NUM=$((START_LINE - 1))
-tail -n +$START_LINE "$CSV_FILE" | while IFS=',' read -r PROTEIN LIGAND MODEL; do
-    ((LINE_NUM++))
-
-    echo "[INFO] Processing CSV line $LINE_NUM"
-
-    # Trim leading/trailing spaces
-    PROTEIN=$(echo "$PROTEIN" | xargs)
-    LIGAND=$(echo "$LIGAND" | xargs)
-    MODEL=$(echo "$MODEL" | xargs)
-    
-    # Take only the last part of the model name after the last '/'
-    MODEL_SHORT=${MODEL##*/}
-    echo "Model='$MODEL'"
-
-    # Handle missing ligand
-    if [[ "$LIGAND" == "" || "$LIGAND" == "None" || "$LIGAND" == "none" ]]; then
-        LIG_ARG="None"
-    else
-        LIG_ARG="$LIGAND"
-    fi
-
-    for RUN in 1 2 3; do
-        
-        LOGFILE="agent_logs/${PROTEIN}_${LIG_ARG}_${MODEL_SHORT}_run${RUN}.log"
-
-        echo "------------------------------------------------------"
-        echo "[INFO] Running: Protein=$PROTEIN | Ligand=$LIG_ARG | Model=$MODEL (Repeat $RUN/3)"
-        echo "[INFO] Output → $LOGFILE"
-        echo "------------------------------------------------------"
-
-        # Run the Python script
-        if ! python main.py \
-            --pdb_id "$PROTEIN" \
-            --ligand "$LIG_ARG" \
-            --model "$MODEL" \
-            --temp 300 \
-            --duration 0.01 \
-            > "$LOGFILE" 2>&1
-        then
-            echo "[WARN] DynaMate failed for $PROTEIN $LIG_ARG, run $RUN."  | tee -a "$FAILED_SYSTEMS"
-        fi
-
-        echo "[INFO] Finished run $RUN for $PROTEIN ($MODEL)."
-
-    done
-
-    # Save progress
-    echo $((LINE_NUM + 1)) > "$CHECKPOINT"
-
-done
-
-echo "[INFO] All runs completed!"

From 61ac0889062da954c1c5422c33fa701ecb1ae00e Mon Sep 17 00:00:00 2001
From: Cassandra Masschelein <cassandramasschelein@gmail.com>
Date: Mon, 11 May 2026 16:43:48 +0200
Subject: [PATCH 07/14] remove useless imports

---
 src/agents/agent.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/agents/agent.py b/src/agents/agent.py
index 56bb5de..a9eeeb5 100644
--- a/src/agents/agent.py
+++ b/src/agents/agent.py
@@ -1,5 +1,4 @@
 import os
-import time
 from pathlib import Path
 from typing import Dict, Any, List
 import json

From 1f11d88f08d1ebd06069fe6ac426c4b576d55445 Mon Sep 17 00:00:00 2001
From: Cassandra Masschelein <cassandramasschelein@gmail.com>
Date: Wed, 13 May 2026 14:51:55 +0200
Subject: [PATCH 08/14] add sandbox path

---
 src/tools/pdb_tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tools/pdb_tools.py b/src/tools/pdb_tools.py
index c433c7d..071574b 100644
--- a/src/tools/pdb_tools.py
+++ b/src/tools/pdb_tools.py
@@ -205,7 +205,7 @@ def prepare_pdb_file_ligand(sandbox_dir: str, pdb_id: str, ligand_name: str = No
             else:
                 index = ligand_pdb_file.split("_")[-1].split(".")[0]  # get index from filename
                 protonated_file = f"{sandbox_dir}/{ligand_name}_{index}_h.pdb"
-                list_protonated_files.append(f"{ligand_name}_{index}_h.pdb")
+                list_protonated_files.append(f"{sandbox_dir}/{ligand_name}_{index}_h.pdb")
             
             cmd = shlex.split(f"obabel {ligand_pdb_file} -O {protonated_file} -p7")
             result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)

From 448b7a358a682e8fccae53601741aebe0e64fb6e Mon Sep 17 00:00:00 2001
From: Cassandra Masschelein <cassandramasschelein@gmail.com>
Date: Sat, 4 Jul 2026 00:34:26 +0200
Subject: [PATCH 09/14] update tleap script

---
 src/scripts/run_tleap.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/scripts/run_tleap.sh b/src/scripts/run_tleap.sh
index 8416710..b090866 100755
--- a/src/scripts/run_tleap.sh
+++ b/src/scripts/run_tleap.sh
@@ -13,6 +13,8 @@ PDB_ID=$3
 # Create tleap input file
 cat > leap.in << EOF
 source leaprc.protein.ff14SB
+# Load DNA parameters to support DNA residues (DA/DC/DG/DT)
+source leaprc.DNA.bsc1
 source leaprc.water.tip3p
 
 # Map PDB atom names to template atom names
@@ -38,4 +40,4 @@ if [ $? -ne 0 ]; then
     echo "tleap failed to generate output files."
 else
     echo "${PDBFILE} processed. Generated ${PDB_ID}.prmtop, ${PDB_ID}.inpcrd, and ${PDB_ID}_tleap.pdb."
-fi
\ No newline at end of file
+fi

From 13c6080bb5c0d2dc4c802673b15ea83eb93d3e25 Mon Sep 17 00:00:00 2001
From: Cassandra Masschelein <cassandramasschelein@gmail.com>
Date: Sat, 4 Jul 2026 00:54:54 +0200
Subject: [PATCH 10/14] remove automated pipeline inputs

---
 main.py                  |  2 +-
 src/agents/md_agent.py   |  9 +++------
 src/agents/prep_agent.py | 16 +++-------------
 src/constants.py         |  2 +-
 4 files changed, 8 insertions(+), 21 deletions(-)

diff --git a/main.py b/main.py
index 3548357..ebe1801 100644
--- a/main.py
+++ b/main.py
@@ -20,7 +20,7 @@ def _ensure_api_key(env_var: str, prompt_name: str) -> str | None:
     key = os.environ.get(env_var)
 
     if not key:
-        print(f"--- Missing API Key: {prompt_name} ---")
+        print(f"Missing API Key: {prompt_name}")
         key = input(f"Please enter your {prompt_name} API key: ").strip()
         if key:
             os.environ[env_var] = key
diff --git a/src/agents/md_agent.py b/src/agents/md_agent.py
index 8a35b22..82e8d6b 100644
--- a/src/agents/md_agent.py
+++ b/src/agents/md_agent.py
@@ -223,8 +223,7 @@ def _run_agent(self, remaining_steps: list[str]):
 
             if iteration == MAX_ITERATIONS:
                 print(f"\n[Warning] Pipeline has reached {MAX_ITERATIONS} iterations without completing.")
-                # answer = input("Would you like to quit and get a summary of what went wrong? (yes/no): ").strip().lower()
-                answer = "yes"
+                answer = input("Would you like to quit and get a summary of what went wrong? (yes/no): ").strip().lower()
                 if answer in ("yes", "y"):
                     self.logger.info(f"User chose to quit after {iteration} iterations.")
                     return
@@ -245,8 +244,7 @@ def _run_agent(self, remaining_steps: list[str]):
                         print(f"\nAgent: {response.content}")
                     else:
                         print("\nAgent: I need your input to continue.")
-                    # user_input = input("You: ").strip()
-                    user_input = "No input provided, please make your own decision to help the pipeline continue."
+                    user_input = input("You: ").strip()
                     self.messages.append({"role": "user", "content": user_input})
 
             except Exception as e:
@@ -278,8 +276,7 @@ def _run_agent(self, remaining_steps: list[str]):
                     self.messages.append({"role": "assistant", "content": response.content})
                     if response.content:
                         print(f"\nAgent: {response.content}")
-                    # user_input = input("You (press Enter to exit): ").strip()
-                    user_input = None
+                    user_input = input("You (press Enter to exit): ").strip()
                     if not user_input:
                         self.logger.info("User exited post-pipeline conversation.")
                         break
diff --git a/src/agents/prep_agent.py b/src/agents/prep_agent.py
index af82bc2..d9b57ff 100644
--- a/src/agents/prep_agent.py
+++ b/src/agents/prep_agent.py
@@ -70,7 +70,6 @@ def _setup_system_prompt(self) -> None:
 
     def _ask_for_system(self):
         """Have the LLM ask the user for the PDB ID and optional ligand, parse via LLM, then confirm."""
-        # Step 1: LLM asks the user
         self.messages.append({
             "role": "user",
             "content": "Ask the user what molecular system they would like to simulate (PDB ID or file upload) and whether they have a ligand to include (3-letter code).",
@@ -83,7 +82,6 @@ def _ask_for_system(self):
             user_input = input("You: ").strip()
             self.messages.append({"role": "user", "content": user_input})
 
-            # Step 2: LLM extracts PDB ID and ligand as JSON
             parse_messages = [
                 {
                     "role": "user",
@@ -108,7 +106,6 @@ def _ask_for_system(self):
             except (json.JSONDecodeError, AttributeError):
                 pdb_id, ligand = None, None
 
-            # Step 3: Confirm with user
             confirm_parts = [f"PDB ID: {pdb_id or 'not found'}"]
             confirm_parts.append(f"Ligand: {ligand}" if ligand else "Ligand: none")
             print(f"\nAgent: I understood the following — {', '.join(confirm_parts)}. Is that correct? (yes/no)")
@@ -141,8 +138,7 @@ def _get_pdb_file_path(self, prompt):
                 self.messages.append({"role": "assistant", "content": response.content})
                 if response.content:
                     print(f"\nAgent: {response.content}")
-                user_input = "No input provided, please make your own decision to help the pipeline continue."
-                # user_input = input("You: ").strip()
+                user_input = input("You: ").strip()
                 if user_input:
                     self.messages.append({"role": "user", "content": user_input})
 
@@ -235,10 +231,7 @@ def _calculate_duration(self):
     def _generate_plan(self, temperature, duration):
         if self.ligand_name:
             steps = [
-                {
-                    "step": "prepare_pdb_file_ligand",
-                    "description": "Clean and preprocess PDB file for protein-ligand system.",
-                },
+                {"step": "prepare_pdb_file_ligand", "description": "Clean and preprocess PDB file for protein-ligand system"},
                 {"step": "add_caps", "description": "Add N- and C-terminal capping groups."},
                 {"step": "rename_histidines", "description": "Rename HIS to HIE, HIP or HID."},
                 {"step": "param_ligand", "description": "Generate ligand parameters using antechamber or acpype."},
@@ -249,10 +242,7 @@ def _generate_plan(self, temperature, duration):
             ]
         else:
             steps = [
-                {
-                    "step": "prepare_pdb_file_ligand",
-                    "description": "Clean and preprocess PDB file for protein-only system.",
-                },
+                {"step": "prepare_pdb_file_ligand","description": "Clean and preprocess PDB file for protein-only system."},
                 {"step": "add_caps", "description": "Add N- and C-terminal capping groups."},
                 {"step": "rename_histidines", "description": "Rename HIS to HIE, HIP or HID."},
                 {"step": "run_tleap", "description": "Build system topology and solvate complex using tleap."},
diff --git a/src/constants.py b/src/constants.py
index 759f994..c5421e7 100644
--- a/src/constants.py
+++ b/src/constants.py
@@ -5,7 +5,7 @@
 SUMMARY_OUTPUT_TOKENS = 6000
 MAX_CONTEXT_TOKENS = 32000
 PAPER_DIR = Path(__file__).resolve().parent.parent / "my_papers"
-MODEL_NAME = "openrouter/openai/gpt-4.1-2025-04-14"
+MODEL_NAME = "openrouter/openai/gpt-5.5"
 TEMPERATURE = 0.1
 
 SCRIPTS_DIR = Path(__file__).resolve().parent / "scripts"

From aef94bb40ba0221a026360ae94ace49e55ec6f10 Mon Sep 17 00:00:00 2001
From: Bohdan Naida <bohdan.naida@gmail.com>
Date: Tue, 7 Jul 2026 13:33:00 +0200
Subject: [PATCH 11/14] fix: update docker

---
 docker/Dockerfile      | 10 ++++++++--
 docker/entrypoint.sh   |  7 ++++++-
 src/tools/pdb_tools.py |  3 ++-
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 1df482e..60c0c0b 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM md_software:latest
+FROM bohdannaida/md_software:latest
 
 RUN apt-get update && apt-get install -y \
     openbabel \
@@ -24,12 +24,18 @@ RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkg
 COPY environment.yml /tmp/environment.yml
 RUN conda env create -f /tmp/environment.yml && \
     conda clean -afy
+# Separate env for MM/PB(GB)SA binding affinity
+COPY gmx_MMPBSA/env.yml /tmp/gmxmmpbsa.yml
+RUN conda env create -f /tmp/gmxmmpbsa.yml && \
+    conda clean -afy
+ENV MMPBSA_ENV_DIR="/opt/conda/envs/gmxMMPBSA/bin/gmx_MMPBSA"
 
-ARG CONDA_ENV_NAME=dynagent
+ARG CONDA_ENV_NAME=dynamate
 ENV CONDA_DEFAULT_ENV=$CONDA_ENV_NAME
 ENV PATH="$CONDA_DIR/envs/$CONDA_ENV_NAME/bin:$PATH"
 
 
+
 # Create a new user for the agent
 ARG AGENT_USER=beautifulagent
 RUN useradd -m $AGENT_USER
diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
index 37e0dd5..2b96523 100644
--- a/docker/entrypoint.sh
+++ b/docker/entrypoint.sh
@@ -1,5 +1,10 @@
 #!/bin/bash
 source /opt/conda/etc/profile.d/conda.sh
-conda activate dynagent
+conda activate dynamate
 source /opt/software/ambertools25/amber.sh
+
+# First arg is a flag (e.g. --model) -> run the agent; else exec it (e.g. /bin/bash)
+if [ "${1:0:1}" = '-' ]; then
+    set -- python /app/main.py "$@"
+fi
 exec "$@"
\ No newline at end of file
diff --git a/src/tools/pdb_tools.py b/src/tools/pdb_tools.py
index 071574b..22b80ca 100644
--- a/src/tools/pdb_tools.py
+++ b/src/tools/pdb_tools.py
@@ -205,7 +205,8 @@ def prepare_pdb_file_ligand(sandbox_dir: str, pdb_id: str, ligand_name: str = No
             else:
                 index = ligand_pdb_file.split("_")[-1].split(".")[0]  # get index from filename
                 protonated_file = f"{sandbox_dir}/{ligand_name}_{index}_h.pdb"
-                list_protonated_files.append(f"{sandbox_dir}/{ligand_name}_{index}_h.pdb")
+
+            list_protonated_files.append(protonated_file)
             
             cmd = shlex.split(f"obabel {ligand_pdb_file} -O {protonated_file} -p7")
             result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)

From 94ceb816bf6509c6a0cdc41a80d444e2e96ec734 Mon Sep 17 00:00:00 2001
From: Bohdan Naida <bohdan.naida@gmail.com>
Date: Tue, 7 Jul 2026 14:25:18 +0200
Subject: [PATCH 12/14] make MMPBSA use the environment direction defined as
 the env variable

---
 src/tools/MMPBSA.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/tools/MMPBSA.py b/src/tools/MMPBSA.py
index af0cd81..9287f37 100644
--- a/src/tools/MMPBSA.py
+++ b/src/tools/MMPBSA.py
@@ -73,9 +73,10 @@ def run_gmxMMPBSA(sandbox_dir: str, pdb_id: str, nsteps:str, nstxout_compressed:
     xtc_file=f"{sandbox_dir}/md_noPBC.xtc"
     index_file=f"{sandbox_dir}/index.ndx"
     topol_file=f"{sandbox_dir}/topol.top"
+    MMPBSA_ENV_DIR=os.environ.get("MMPBSA_ENV_DIR", str(constants.MMPBSA_ENV_DIR))
 
     cmd = [
-        constants.MMPBSA_ENV_DIR,
+        MMPBSA_ENV_DIR,
         "-O",
         "-i", "mmpbsa.in",
         "-cs", tpr_file,

From 09540d1b53505fbb4f8ad9d3836e7bbb71bb7752 Mon Sep 17 00:00:00 2001
From: Bohdan Naida <bohdan.naida@gmail.com>
Date: Tue, 7 Jul 2026 15:24:24 +0200
Subject: [PATCH 13/14] fix: make the system ask for OpenAI key only if there
 are documents we need to embed

---
 src/tools/RAG_tools.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/tools/RAG_tools.py b/src/tools/RAG_tools.py
index c106490..b6a1ea6 100644
--- a/src/tools/RAG_tools.py
+++ b/src/tools/RAG_tools.py
@@ -23,15 +23,15 @@ def _ensure_openai_key() -> None:
 
 
 def _load_documents() -> Docs:
-    _ensure_openai_key()
-    docs = Docs()
-
     pdf_files = list(constants.PAPER_DIR.rglob("*.pdf")) if constants.PAPER_DIR.exists() else []
     total_files = len(pdf_files)
 
     if total_files == 0:
         return None
 
+    _ensure_openai_key()  # only needed once we actually have papers to embed
+    docs = Docs()
+
     pickled_docs = "my_docs.pkl"
 
     if not os.path.exists(pickled_docs):
@@ -56,7 +56,6 @@ def _load_documents() -> Docs:
 
 def search_papers(query: dict):
     global documents
-    _ensure_openai_key()
 
     if not documents:
         documents = _load_documents()

From f0de3fe871635884e71aef4b9add9ecbe1083c23 Mon Sep 17 00:00:00 2001
From: Bohdan Naida <bohdan.naida@gmail.com>
Date: Tue, 7 Jul 2026 16:48:36 +0200
Subject: [PATCH 14/14] make docker work well on the cluster

---
 docker/Dockerfile  | 1 +
 gmx_MMPBSA/env.yml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 60c0c0b..38568b8 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -15,6 +15,7 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -
     bash /tmp/miniconda.sh -b -p $CONDA_DIR && \
     rm /tmp/miniconda.sh
 ENV PATH="$CONDA_DIR/bin:$PATH"
+ENV CONDA_FETCH_THREADS=1
 
 # Accept Conda's Terms and Conditions
 
diff --git a/gmx_MMPBSA/env.yml b/gmx_MMPBSA/env.yml
index e394468..1f9a9ef 100644
--- a/gmx_MMPBSA/env.yml
+++ b/gmx_MMPBSA/env.yml
@@ -6,6 +6,7 @@ dependencies:
   - python=3.9
   - pip
   - ambertools<=23.3
+  - mpich
   - mpi4py<=3.1.5
   - gromacs<=2023.4
   - git