call chainbuild
endif
C Following 2 lines for diagnostics; comment out if not needed
- write (iout,*) "After sideadd"
- call intout
+c write (iout,*) "After sideadd"
+c call intout
endif
if (indpdb.eq.0) then
C Read sequence if not taken from the pdb file.
do i=1,nres
itype(i)=rescode(i,sequence(i),iscode)
enddo
+ if (itype(2).eq.10.and.itype(1).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the first full residue, initial dummy deleted"
+ do i=1,nres
+ itype(i)=itype(i+1)
+ enddo
+ nres=nres-1
+ endif
+ if (itype(nres-1).eq.10.and.itype(nres).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the last full residue, terminal dummy deleted"
+ nres=nres-1
+ endif
+
C Assign initial virtual bond lengths
do i=2,nres
vbld(i)=vbl
c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
if (constr_dist.gt.0) then
call read_dist_constr
- call hpb_partition
endif
+ if (nhpb.gt.0) call hpb_partition
c write (iout,*) "After read_dist_constr nhpb",nhpb
c call flush(iout)
if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
write (iout,'(20i4)') (iss(i),i=1,ns)
if (dyn_ss) then
write(iout,*)"Running with dynamic disulfide-bond formation"
- do i=nss+1,nhpb
- ihpb(i-nss)=ihpb(i)
- jhpb(i-nss)=jhpb(i)
- forcon(i-nss)=forcon(i)
- dhpb(i-nss)=dhpb(i)
- enddo
- nhpb=nhpb-nss
- nss=0
- call hpb_partition
- do i=1,ns
- dyn_ss_mask(iss(i))=.true.
- enddo
else
write (iout,'(/a/)') 'Pre-formed links are:'
do i=1,nss
i2=jhpb(i)-nres
it1=itype(i1)
it2=itype(i2)
- if (me.eq.king.or..not.out1file)
- & write (iout,'(2a,i3,3a,i3,a,3f10.3)')
+ 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
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+ enddo
+ endif
if (i2ndstr.gt.0) call secstrp2dihc
c call geom_to_var(nvar,x)
c call etotal(energia(0))
C Read preformed bridges.
if (ns.gt.0) then
read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
- write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
+ if(fg_rank.eq.0)
+ & write(iout,*)'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
if (nss.gt.0) then
nhpb=nss
C Check if the residues involved in bridges are in the specified list of
if (wfrag_(i).gt.0.0d0) then
do j=ifrag_(1,i),ifrag_(2,i)-1
do k=j+1,ifrag_(2,i)
- write (iout,*) "j",j," k",k
+c write (iout,*) "j",j," k",k
ddjk=dist(j,k)
if (constr_dist.eq.1) then
nhpb=nhpb+1