logical :: minim,refstr,pdbref,overlapsc,&
energy_dec,sideadd,lsecondary,read_cart,unres_pdb,&
vdisulf,searchsc,lmuca,dccart,extconf,out1file,&
- gnorm_check,gradout,split_ene,with_theta_constr
+ gnorm_check,gradout,split_ene,with_theta_constr,protein,ions,nucleic
#ifdef CLUSTER
integer :: iopt,nend,nstart,outpdb,outmol2 !cluster
logical :: punch_dist,print_dist,lside,lprint_cart,lprint_int,&