run_netmhcpan_script added

.gitignore

@@ -23,4 +23,5 @@ ProteinMPNN/
 ProteinMPNN/*
 ProteinMPNN/examples
 ProteinMPNN/outputs
-ProteinMPNN/.gitignore
+ProteinMPNN/.gitignore
+user_setting.py

README.md

@@ -24,6 +24,7 @@ sequences.
     CUDA-enabled GPU (required for AlphaFold)
     Modeller (requires a license key)
     Git
+    git-lfs (for large files)
 ```
 
 Follow these steps to set up PMGen on your system:
@@ -32,6 +33,8 @@ Follow these steps to set up PMGen on your system:
    ```bash
    git clone https://github.com/AmirAsgary/PMGen.git
    cd PMGen
+   conda init bash
+   source ~/.bashrc
    bash -l install.sh
    conda activate PMGen
    ```
@@ -43,7 +46,9 @@ Follow these steps to set up PMGen on your system:
 
 Edit `user_setting.py` to adjust netMHCpan and netMHCIIpan installation paths.
 
-
+2. **Tip for installing NetMHCpan**: 
+    - NetMHCpan requires tcsh to be installed. You can install it using `sudo apt-get install tcsh`.
+    - read the readme file in `netMHCpan` folder and follow instructions.
 
 ## Usage