Fix conda installation for ambertools and pymol

Dockerfile

@@ -10,6 +10,12 @@ RUN apt-get update && apt-get install -y \
     make \
     libffi-dev \
     libssl-dev \
+    libgl1-mesa-glx \
+    libglib2.0-0 \
+    libxext6 \
+    libsm6 \
+    libxrender1 \
+    libgomp1 \
     && rm -rf /var/lib/apt/lists/*
 
 # Install conda
@@ -19,11 +25,15 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &
 
 ENV PATH="/opt/conda/bin:${PATH}"
 
-# Install AMBER tools and PyMOL via conda
-RUN conda install -c conda-forge -c bioconda \
-    ambertools \
-    pymol-open-source \
-    -y
+# Update conda and install packages with retry logic
+RUN conda update -n base -c defaults conda -y && \
+    conda config --add channels conda-forge && \
+    conda config --add channels bioconda && \
+    conda config --set channel_priority flexible
+
+# Install AMBER tools and PyMOL with proper conda syntax
+RUN conda install conda-forge::ambertools -y --timeout 300 && \
+    conda install conda-forge::pymol-open-source -y --timeout 300
 
 # Install Python packages via pip
 RUN pip install --no-cache-dir \