        #GENERAL

root      PHD

multitrj      n
root_multitrj

run                     1                               #options: integer

RecoverJobs            y                                #options: y,n

Cpath                  /usr/local/common/bin	
Apath                  /usr/local/common/bin
Gpath		    /usr/local/common/share/gromacs4.6.3/bin


	#FFIELD

use_topology            n                               #options: y,n
	itp_receptor  trp.itp
	itp_ligand    ben.itp
use_nonstd_ff           y                               #options: y,n
ffield                 


        #GROMACS VARIABLE

complex	                complex
receptor                phd1
ligand                  tail

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                    1                               #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                     y                               #options: y,n
MUTATION        PHD          9             ASP     receptor ASP9ALA
MUTATION        PHD         8             ARG     lig       ARG8ALA
