integer modecalc,iscode,indpdb,indback,indphi,iranconf,icheckgrad,
- & inprint,i2ndstr,mucadyn,constr_dist,constr_homology,homol_nset
- real*8 waga_dist1,waga_angle1
- real*8 waga_dist, waga_angle, waga_theta, waga_d, dist_cut
+ & iprint,i2ndstr,mucadyn,constr_dist,constr_homology,homol_nset
+ real*8 waga_homology
+ real*8 waga_dist, waga_angle, waga_theta, waga_d, dist_cut,
+ & dist2_cut,checkgrad_inc
logical minim,refstr,pdbref,outpdb,outmol2,outx,overlapsc,
& energy_dec,
& sideadd,lsecondary,read_cart,unres_pdb,
& vdisulf,searchsc,lmuca,dccart,extconf,out1file,
- & gnorm_check,gradout,split_ene
+ & gnorm_check,gradout,split_ene,read2sigma
+ & ,start_from_model
common /cntrl/ modecalc,iscode,indpdb,indback,indphi,iranconf,
& icheckgrad,minim,i2ndstr,refstr,pdbref,outpdb,outmol2,outx,
- & iprint,
+ & iprint,checkgrad_inc,
& overlapsc,energy_dec,sideadd,lsecondary,read_cart,unres_pdb
& ,vdisulf,searchsc,lmuca,dccart,mucadyn,extconf,out1file,
& constr_dist,gnorm_check,gradout,split_ene,constr_homology,
- & homol_nset
- common /homol/ waga_dist1(maxprocs/20), waga_angle1(maxprocs/20),
- & waga_dist, waga_angle, waga_theta, waga_d, dist_cut
+ & homol_nset,read2sigma,start_from_model
+ common /homol/ waga_homology(maxprocs/20),
+ & waga_dist, waga_angle, waga_theta, waga_d, dist_cut,dist2_cut
C... minim = .true. means DO minimization.
C... energy_dec = .true. means print energy decomposition matrix