inputfile.in

*PDB INFORMATION

PDB FILENAME= ./Example/pdb1lxa.ent
PROTEIN CHAIN= A

MULTIMER PROTEIN MODE = 0
HOMOOLIGOMER = 1
ALIGNMENT FILE = ./Example/lpxa70.fasta
*leaving empy the ALIGNMENT FILE only de pdb sequence will be taken for the simulations


*RUN INFORMATION

BETA FROM LIST = 0
LIST NAME = betalistshort.dat
INITIAL BETA PARAMETER= 0.25
SCREENING BETA-STEP= 5.0
MAXIMUM BETA= 0.40 

MUTATION MATRIX= qijHKY-lpxa.dat


INITIAL NUMBER OF ACCEPTED SUSTITUTIONS PER SITE= 20.0.0
STEP OF ACCEPTED SUSTITUTIONS PER SITE= 10.0
MAXIMUM NUMBER OF ACCEPTED SUSTITUTIONS PER SITE= 21.0
NUMBER OF INDEPENDENT RUNS= 18000

*OUTPUT INFORMATION

RESULTS FILENAME= lpxaM

*Name to be printed in HYPHY input matrices
MODEL NAME = scpem

PATH TO RESULTS = ./OUT