        #GENERAL

root      1EBZ

multitrj      n
root_multitrj

run                     1                               #options: integer

RecoverJobs            y                                #options: y,n

Cpath                  /home/users/ntu/n1805727/APBS/share/tools/manip	
Apath                  /home/users/ntu/n1805727/APBS/bin
Gpath		    /home/users/ntu/n1805727/GMX5.1.4_Mine/gromacs-5.1.4-cpu/bin


	#FFIELD

use_topology            y                               #options: y,n
	itp_receptor  Protein.itp
	itp_receptor  Protein2.itp
	itp_ligand    BEC.itp
use_nonstd_ff           n                               #options: y,n
ffield                 6


        #GROMACS VARIABLE

complex	                System
receptor                Protein
ligand                  BEC

skip                    1                               #options: integer
min                     n                               #options: y,n

double_p                n                               #options: y,n


        #APBS VARIABLE

coulomb                  coul                     #options: coul,gmx

linearized              n                               #options: y,n
precF                   1                               #options: integer 1,2,3(..)
temp                    300
bcfl                    sdh                             #options: sdh,mdh,focus
pdie                    2                               #options: integer, usually between 1 and 20


       #QUEQUE VARIABLE
	
cluster                 n                             #options: y,n
Q                       ...                                     #necessary only if cluster="y"!!

mnp                     1                             #options: integer 


       #OUTPUT VARIABLE
pdf                     n                               #options: y,n


       # ALANINE SCANNING

cas                     n                               #options: y,n
	
#MUTATION        P53          112             PHE lig PHE112ALA
#MUTATION        P53          115             LEU lig LEU115ALA
#MUTATION        P53          116             TRP lig TRP116ALA
#MUTATION        P53          119             LEU lig LEU119ALA
