goto 10
else if (card(:3).eq.'TER') then
C End current chain
- ires_old=ires+1
+c ires_old=ires+1
+ ires_old=ires+2
+ itype(ires_old-1)=ntyp1
itype(ires_old)=ntyp1
ibeg=2
c write (iout,*) "Chain ended",ires,ishift,ires_old
nres=ires
do i=2,nres-1
c write (iout,*) i,itype(i)
+
if (itype(i).eq.ntyp1) then
-c write (iout,*) "dummy",i,itype(i)
- do j=1,3
- c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
-c c(j,i)=(c(j,i-1)+c(j,i+1))/2
- dc(j,i)=c(j,i)
- enddo
- endif
+ if (itype(i+1).eq.ntyp1) then
+C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+C if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+C call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+C if (fail) then
+C e2(1)=0.0d0
+C e2(2)=1.0d0
+C e2(3)=0.0d0
+C endif !fail
+C do j=1,3
+C c(j,i)=c(j,i-1)-1.9d0*e2(j)
+C enddo
+C else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i-2)-c(j,i-3))/2.0
+ c(j,i)=c(j,i-1)+dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+C endif !unres_pdb
+ else !itype(i+1).eq.ntyp1
+C if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+C call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+C if (fail) then
+C e2(1)=0.0d0
+C e2(2)=1.0d0
+C e2(3)=0.0d0
+C endif
+C do j=1,3
+C c(j,i)=c(j,i+1)-1.9d0*e2(j)
+C enddo
+C else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i+3)-c(j,i+2))/2.0
+ c(j,i)=c(j,i+1)-dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+C endif !unres_pdb
+ endif !itype(i+1).eq.ntyp1
+ endif !itype.eq.ntyp1
enddo
C Calculate the CM of the last side chain.
call sccenter(ires,iii,sccor)
nres=nres+1
itype(nres)=ntyp1
do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
nsup=nsup-1
nstart_sup=2
do j=1,3
- dcj=c(j,4)-c(j,3)
+ dcj=(c(j,4)-c(j,3))/2.0
c(j,1)=c(j,2)-dcj
c(j,nres+1)=c(j,1)
enddo
lll=lll+1
cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
- if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
+ if ((itype(i-1).eq.ntyp1).and.(i.gt.2).and.(i.ne.nres)) then
chain_length=lll-1
kkk=kkk+1
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
endif
enddo
enddo
+ if (chain_length.eq.0) chain_length=nres
+ write (iout,*) chain_length
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)