fixed documentation on need to output both force and coordinate to th…

…e same file

README.md

@@ -19,6 +19,11 @@ See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest
 pip install CodeEntropy
 ```
 
+### Input
+For supported format (AMBER NETCDF and GROMACS TRR) you will need to output the **coordinates** and **forces** to the **same file**.
+
+See [Format overview — MDAnalysis User Guide documentation](https://userguide.mdanalysis.org/stable/formats/index.html)
+
 ### Command-line tool
 A quick and easy way to get started is to use the command-line tool which you can run in bash by simply typing `CodeEntropyPoseidon` (Note: this doesn't work on Windows!!!)
 #### For help
@@ -28,7 +33,7 @@ CodeEntropyPoseidon -h
 #### Arguments
 | Arguments  | Description | Default | type|
 | ------------- | ------------- |----------- |--------------|
-| `-f`, `--top_traj_file`  | Path to Structure/topology file (AMBER PRMTOP or GROMACS TPR) followed by Trajectory file(s)  | Requires either `--top_traj_file` or `--pickle`  | list of `str` |
+| `-f`, `--top_traj_file`  | Path to Structure/topology file (AMBER PRMTOP or GROMACS TPR) followed by Trajectory file(s) (AMBER NETCDF or GROMACS TRR). You will need to output the **coordinates** and **forces** to the **same file**  | Require at least 2 file: a topology and a trajectory file | list of `str` |
 | `-l`, `--selectString`  | Selection string for CodeEntropy such as protein or resid, refer to `MDAnalysis.select_atoms` for more information. | `"all"`: select all atom in trajectory for CodeEntropy analysis for trajectory without solvent  | `str` |
 | `-b`, `--begin`  | Start analysing the trajectory from this frame index. | `0`: From begining | `int` |
 | `-e`, `--end`  | Stop analysing the trajectory at this frame index | `-1`: end of trajectory | `int` |
@@ -55,6 +60,7 @@ CodeEntropyPoseidon -h
 | `--soluatom`  | Do solution entropy calculation at united atom level (A heavy atom and its covalently bonded H-atoms for an united atom and represent a bead.).  | Flag, activate when included | Flag |
 | `--solContact`  | Do solute contact calculation.  | Flag, activate when included | Flag |
 #### Example 
+You need to clone this repository to download example trajectories.
 ```
 # example 1 DNA
 CodeEntropyPoseidon -f "Example/data/md_A4_dna.tpr" "Example/data/md_A4_dna_xf.trr" -a "C5'" "C4'" "C3'" -l "all" -t 8 --wm --res --uatom --topog 3

docs/Run_as_script.rst

@@ -2,6 +2,8 @@ Run As Script
 =================
 CodeEntropy can also be run as a script for more advanced operations.
 
+.. _load-custom:
+
 1. Loading data
 -------------------
 First you should load the data into an MDanalysis universe. For this code, MDanalysis must be able to read dihedral and force directly from the trajectory files 

docs/getting_started.rst

@@ -16,6 +16,12 @@ Run the following at the root directory of this repository
 
     pip install CodeEntropy
 
+Input
+----------
+For supported format (AMBER NETCDF and GROMACS TRR) you will need to output the **coordinates** and **forces** to the **same file**.
+
+For unsupported format see :ref:`load-custom` for ideas on how to load custom data into MDanalysis universe and convert to supported format.
+
 Units
 ------------
 The program assumes the following default unit
@@ -65,7 +71,7 @@ Arguments
      - Default
      - Type
    * - ``-f``, ``--top_traj_file`` 
-     - Path to Structure/topology file(``AMBER PRMTOP``, ``GROMACS TPR`` or topology file with MDAnalysis readable dihedral information (not officially supported)) followed by Trajectory file(s) (``GROMAC TRR`` or ``AMBER NETCDF``)
+     - Path to Structure/topology file(``AMBER PRMTOP``, ``GROMACS TPR`` or topology file with MDAnalysis readable dihedral information (not officially supported)) followed by Trajectory file(s) (``GROMAC TRR`` or ``AMBER NETCDF``) You will need to output the **coordinates** and **forces** to the **same file** . 
      - Required
      - list of ``str`` 
    * - ``-l``, ``--selectString``

scripts/CodeEntropyPoseidon

@@ -43,7 +43,7 @@ try:
 						dest="filePath",
 						action='store',
 						nargs='+',
-						help="Path to Structure/topology file (AMBER PRMTOP, GROMACS TPR which contains topology and dihedral information) followed by Trajectory file(s) (AMBER NETCDF or GROMACS TRR). Required.")
+						help="Path to Structure/topology file (AMBER PRMTOP, GROMACS TPR which contains topology and dihedral information) followed by Trajectory file(s) (AMBER NETCDF or GROMACS TRR) you will need to output the coordinates and forces to the same file. Required.")
 	parser.add_argument('-l', '--selectString', 
 						action='store',
 						dest="selectionString",