why ligand is getting detached from protein at the complex.gro step when I am generating the ligand toplogy from ATB , swissparam, acpype serverserver? while this problem did not occur while using prodrg.
Kindly suggest
Sivasakthi Paramasivam
Dear Priyanka Choudhary
Kindly try to check the coordinates of your ligand and Generate topology files using CGENFF or CHARMM-GUI!
After generating. str file from Cgenff
Run this script to install Python 3.5 as an error generates while generating ligand topology.
apt-get install python3.5
pip uninstall pip
wget https://bootstrap.pypa.io/pip/3.5/get-pip.py
python3.5 get-pip.py
pip -V
pip install numpy
pip install networkx==2.3
pwd
then run the script
python3.5 cgenff_charmm2gmx.py Ligand Ligand.mol2 Ligand.str charmm36-jul2022.ff
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