README file for the conversion of the downloaded PDB file to CHARMM
coordinate file.

Step 1: The example pdb file has ten structures for the RNA. Extract the first
set of coordinates and create a file (rr_1.pdb)

Step 2: Use the following command to delete the hydrogens. Hydrogens will
be added when generating the RNA using CHARMM.

awk '{if ($3!~/H/) print}' rr_1.pdb > rr_1_noh.pdb

Step 3: Compile the FORTRAN code (conv_pdb_charmm_prot.f) and execute
	You will read "Give input PDB files, output will be .crd"
	Type the pdb file name (rr_1_noh.pdb). The CHARMM coordinate
	file will be rr_1_noh.pdb.crd

Step 4: In the crd file the following modifications are to be done to 
be read by CHARMM.
  Replace * by ' in the atom names (use the command ":g/*  /s//'  /g" in vi)
  Replace G by GUA (use the command ":g/  G /s//GUA /g" in vi)
  Replace A by ADE 
  Replace C by CYT
  Replace U by URA

Use the resulting in the rr_gen.inp script.