Problems with IFP_generation_examples_TRAJ.ipynb

[PatWalters]

I get an exception when running the cell below "2.2 Computation of PL IFPs for all equilibration trajectories (takes about 15 min)"

---

IndexError Traceback (most recent call last)
in
15 # Save and visualize the IFP dataframe to the specified location
16 # In the RMSD plot, in addition to the protein and ligand (heavy atoms) RMSD, also RMSD of the protein fragments given as an input (auxi_selection) are shown
---> 17 IFP_table = tr.namd.IFP_save(tr.PRJ_DIR+out_name+"_NAMD_com.pkl")
18

~/software/MD-IFP/Scripts/Trajectories.py in IFP_save(self, file, subset)
435 IFP_list = self.IFP_unify(subset)
436 # print("+++++++++++++++++",self.names,subset)
--> 437 n_auxi = len(r_subset[0].rmsd_auxi)
438 for i,(tr_c,n_replica) in enumerate(zip(r_subset,n_subset)):
439 print("# Replica:",i,n_replica)

IndexError: list index out of range

My Data directory looks like this
Data
├── 2YKI
│   ├── 2YKI.pse
│   ├── 2yki.pdb
│   ├── 2yki_MOE.pdb
│   ├── ligand_2yki_MOE.mol2
│   └── ligand_2yki_MOE.pdb
├── 4MQT
│   ├── AMBER_eq
│   │   └── ORTO-CHL-prod8-NPT.pdb
│   ├── IXO.pdb
│   ├── RAMD
│   │   ├── Replica1
│   │   │   ├── Traj1
│   │   │   │   └── ORTO-CHL_108_ramd_016.dcd
│   │   │   └── Traj2
│   │   │   └── ORTO-CHL_104_ramd_016.dcd
│   │   └── Replica2
│   │   ├── Traj1
│   │   │   └── ORTO-CHL_111_ramd_016.dcd
│   │   └── Traj2
│   │   └── ORTO-CHL_105_ramd_016.dcd
│   └── moe.mol2
└── 6EI5
├── INH.pdb
├── amber2namd2.dcd
├── moe.mol2
├── ref-min.pdb
└── ref.prmtop

[DKokh]

The cell "2.2 Computation of PL IFPs for all equilibration trajectories (takes about 15 min)" requires Equilibration data from the archive from NAMD_eq.tar.gz, i.e. your Data should also contain NAMD directory, like this:
Data
├── 4MQT
│ ├── AMBER_eq
│ │ └── ORTO-CHL-prod8-NPT.pdb
│ ├── IXO.pdb
│ ├── RAMD
│ ├── NAMD
│ │ ├── Replica1
│ │ │ └── ORT-CHL_repl.dcd

I added more infromation to the JN