

# Create topology files (*.itp, *.top) and coordinate file (*.gro)

pdb2ItpGroTop.pl  : monomer single domain protein and metalloprotein
pdb2ItpGroTop_multimer_multidomain.pl : multimer and multidomain protein and metalloprotein



# Files used by above perl programs

nbclust_numb.txt :  Amino acid pair and corresponding table number for non-bonded interaction
triplet2cluster.txt : Triplet of secondary structure and corresponding table number for angle interaction 
quartet2cluster.txt : Quartet of secondary structure and corresponding table number for dihedral interaction
quartet2clusterGLY.txt : Quartet of secondary structure related to GLY in second or third place and corresponding table number for GLY dihedral interaction
secstr.exc : binary program file to find secondary structure from PDB file
 


# Example proteins PDB: 
Non metalloprotein :
	1UBQ.pdb
Metalloprotein:
	1DX8.pdb (Zn)
        1CR8.pdb (Ca)
	2CBP.pdb (Cu)
	1SHU.pdb (Mg)
	2DSX.pdb (Fe)
Single chian multi domain
        1D1D.pdb (linker region of two domain 147-152)
Multi chain protein
        1TRL.pdb


For help please see http://pallab.serc.iisc.ernet.in/CGMM/cgmm_home.php
For help please see http://onlinelibrary.wiley.com/doi/10.1002/prot.24609/abstract
