parm /home/databank/MD_traj_dataset/D3PM/sys_md_parameters/batch1/Y/com-dry.pdb
trajin /home/databank/MD_traj_dataset/D3PM/sys_md_parameters/batch1/Y/com-dry.pdb
mask "(:LIG<:5.0)&((!:WAT)&(!:MOL))&(@N,CA,C,O)" maskout mol-5A.dat maskpdb mol-5A.pdb
run