# analysis_pdb



## install environment

```shell
micromamba create -n modeller modeller biopython pymol-open-source biopandas requests ipython ipykernel -y -c conda-forge -c salilab
# modeller注册码：MODELIRANJE (<conda_env>//lib/modeller-10.4/modlib/modeller/config.py)
```

modeller注册码：`MODELIRANJE``

## test 

```shell
cp pdb_test/5isz.pdb pdb_gjm/
gmx_mpi pdb2gmx -f 5isz.pdb -o 5isz.gro -ff amber99sb-ildn -water tip3p -ignh -p topol.top
```