call reada(controlcard,'BOXY',boxysize,100.0d0)
call reada(controlcard,'BOXZ',boxzsize,100.0d0)
c Cutoff range for interactions
- call reada(controlcard,"R_CUT",r_cut,15.0d0)
+ call reada(controlcard,"R_CUT",r_cut,25.0d0)
call reada(controlcard,"LAMBDA",rlamb,0.3d0)
+ write (iout,*) "Cutoff on interactions",r_cut
+ write (iout,*) "lambda",rlamb
call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
if (lipthick.gt.0.0d0) then
print*, 'read_dfa_info finished!'
endif
#endif
+C If the reference structure is not read set the superposition
+C boundaries
+ nstart_sup=nnt
+ nstart_seq=nnt
+ nend_sup=nct
+ nsup=nct-nnt+1
+
if (with_dihed_constr) then
read (inp,*) ndih_constr
c endif
call init_int_table
call setup_var
- write (iout,*) "molread: REFSTR",refstr
- if (refstr) then
- if (.not.pdbref) then
- call read_angles(inp,*38)
- goto 39
- 38 write (iout,'(a)') 'Error reading reference structure.'
-#ifdef MPL
- call mp_stopall(Error_Msg)
-#else
- stop 'Error reading reference structure'
-#endif
- 39 call chainbuild
- nstart_sup=nnt
- nstart_seq=nnt
- nsup=nct-nnt+1
- do i=1,2*nres
- do j=1,3
- cref(j,i)=c(j,i)
- enddo
- enddo
- endif
-c call contact(.true.,ncont_ref,icont_ref)
- endif
- if (ns.gt.0) then
-C write (iout,'(/a,i3,a)')
-C & 'The chain contains',ns,' disulfide-bridging cysteines.'
+ if (ns.gt.0) then
+C write (iout,'(/a,i3,a)')
+C 'The chain contains',ns,' disulfide-bridging cysteines.'
write (iout,'(20i4)') (iss(i),i=1,ns)
- if (dyn_ss) then
+ if (dyn_ss) then
write(iout,*)"Running with dynamic disulfide-bond formation"
- else
- write (iout,'(/a/)') 'Pre-formed links are:'
- do i=1,nss
- i1=ihpb(i)-nres
- i2=jhpb(i)-nres
- it1=itype(i1)
- it2=itype(i2)
- write (iout,'(2a,i3,3a,i3,a,3f10.3)')
- & restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
- & ebr,forcon(i)
- enddo
- write (iout,'(a)')
- endif
+ else
+ write (iout,'(/a/)') 'Pre-formed links are:'
+ do i=1,nss
+ i1=ihpb(i)-nres
+ i2=jhpb(i)-nres
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(2a,i3,3a,i3,a,3f10.3)')
+ & restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
+ & ebr,forcon(i)
+ enddo
+ write (iout,'(a)')
+ endif
endif
if (ns.gt.0.and.dyn_ss) then
do i=nss+1,nhpb