[cleanup] small cleanup

src/agents/md_agent.py

@@ -372,8 +372,7 @@ class MDAgent(BaseAgent):
         if self.ligand_name and success:
         if self.ligand_name and success:
             user_prompt = "\n==========\nWould you like me to calculate the free energy of binding for your protein-ligand system using the MMPBSA tool? (yes/no) \n\n"
             user_prompt = "\n==========\nWould you like me to calculate the free energy of binding for your protein-ligand system using the MMPBSA tool? (yes/no) \n\n"
 
 
-            # user_answer = input(user_prompt).strip().lower()
-            user_answer = "yes"
+            user_answer = input(user_prompt).strip().lower()
 
 
             if user_answer in ("yes", "y"):
             if user_answer in ("yes", "y"):
                 self.logger.info("Running MMPBSA calculation...")
                 self.logger.info("Running MMPBSA calculation...")

src/constants.py

@@ -16,4 +16,4 @@ DATA_DIR = Path(__file__).resolve().parent.parent / "sandbox"
 AGENT_LOGS = Path(__file__).resolve().parent.parent / "agent_logs"
 AGENT_LOGS = Path(__file__).resolve().parent.parent / "agent_logs"
 JSON_LOG_FILE = AGENT_LOGS / "agent_runs.jsonl"
 JSON_LOG_FILE = AGENT_LOGS / "agent_runs.jsonl"
 
 
-MMPBSA_ENV_DIR = Path("/home/hackathon/miniforge3/envs/gmxMMPBSA/bin/gmx_MMPBSA")
+MMPBSA_ENV_DIR = Path("/path/to/your/envs/mmpbsa")
\ No newline at end of file

src/scripts/equil_Gromacs.sh

@@ -96,7 +96,7 @@ if grep -E "system1 +2" topol.top; then #special case for two identical chains n
 		echo "Adding group r_${ranges[0]} to index.ndx" >> $LOG_FILE 2>&1
 		echo "Adding group r_${ranges[0]} to index.ndx" >> $LOG_FILE 2>&1
 		echo -e "ri ${ranges[0]}\nq" | $GMX make_ndx -f em.gro -n index.ndx -o index.ndx >> $LOG_FILE 2>&1
 		echo -e "ri ${ranges[0]}\nq" | $GMX make_ndx -f em.gro -n index.ndx -o index.ndx >> $LOG_FILE 2>&1
 	fi
 	fi
-	if grep -Fq "[ Protein-H_&_r_${ranges[0]} ]" index.ndx; then # -F for fixed string (so can use [] without putting "^\[ r_${ranges[0]} \]", -q for quiet)
+	if grep -Fq "[ Protein-H_&_r_${ranges[0]} ]" index.ndx; then
 		echo "Group Protein-H_&_r_${ranges[0]} already exists in index.ndx" >> $LOG_FILE 2>&1
 		echo "Group Protein-H_&_r_${ranges[0]} already exists in index.ndx" >> $LOG_FILE 2>&1
 	else
 	else
 		echo "Adding group Protein-H_&_r_${ranges[0]} to index.ndx" >> $LOG_FILE 2>&1
 		echo "Adding group Protein-H_&_r_${ranges[0]} to index.ndx" >> $LOG_FILE 2>&1
@@ -105,13 +105,13 @@ if grep -E "system1 +2" topol.top; then #special case for two identical chains n
 else 
 else 
 	i=1
 	i=1
     for range in "${ranges[@]}"; do
     for range in "${ranges[@]}"; do
-        if grep -Fq "[ r_$range ]" index.ndx; then # -F for fixed string (so can use [] without putting "^\[ r_${ranges[0]} \]", -q for quiet)
+        if grep -Fq "[ r_$range ]" index.ndx; then
 			echo "Group r_$range already exists in index.ndx" >> $LOG_FILE 2>&1
 			echo "Group r_$range already exists in index.ndx" >> $LOG_FILE 2>&1
 		else
 		else
 			echo "Adding group r_$range to index.ndx" >> $LOG_FILE 2>&1
 			echo "Adding group r_$range to index.ndx" >> $LOG_FILE 2>&1
 			echo -e "ri $range\nq" | $GMX make_ndx -f em.gro -n index.ndx -o index.ndx >> $LOG_FILE 2>&1
 			echo -e "ri $range\nq" | $GMX make_ndx -f em.gro -n index.ndx -o index.ndx >> $LOG_FILE 2>&1
 		fi
 		fi
-		if grep -Fq "[ Protein-H_&_r_$range ]" index.ndx; then # -F for fixed string (so can use [] without putting "^\[ r_${ranges[0]} \]", -q for quiet)
+		if grep -Fq "[ Protein-H_&_r_$range ]" index.ndx; then
 			echo "Group Protein-H_&_r_$range already exists in index.ndx" >> $LOG_FILE 2>&1
 			echo "Group Protein-H_&_r_$range already exists in index.ndx" >> $LOG_FILE 2>&1
 		else
 		else
 			echo "Adding group Protein-H_&_r_$range to index.ndx" >> $LOG_FILE 2>&1
 			echo "Adding group Protein-H_&_r_$range to index.ndx" >> $LOG_FILE 2>&1