double precision e1(3),e2(3),e3(3)
integer rescode,iterter(maxres),cou
logical fail,sccalc
- integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg
- double precision dcj,efree_temp
+ integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg,ifree
+ double precision dcj!,efree_temp
+ logical zero
bfac=0.0d0
do i=1,maxres
iterter(i)=0
do
read (ipdbin,'(a80)',end=10) card
c write (iout,'(a)') card
+c call flush(iout)
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
sccalc=.true.
endif
! Read free energy
- if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
+c if (index(card,"FREE ENERGY").gt.0) then
+c ifree=index(card,"FREE ENERGY")+12
+c read(card(ifree:),*,err=1115,end=1115) efree_temp
+c 1115 continue
+c endif
! Fish out the ATOM cards.
if (index(card(1:4),'ATOM').gt.0) then
sccalc=.false.
! if (ibeg.eq.0) call sccenter(ires,iii,sccor)
if (ibeg.eq.0) then
c write (iout,*) "Calculating sidechain center iii",iii
+c write (iout,*) "ires",ires
if (unres_pdb) then
+c write (iout,'(i5,3f10.5)') ires,(sccor(j,iii),j=1,3)
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires_old)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
! write (iout,*) "backbone ",atom
#ifdef DEBUG
- write (iout,'(2i3,2x,a,3f8.3)')
+ write (iout,'(i6,i3,2x,a,3f8.3)')
& ires,itype(ires),res,(c(j,ires),j=1,3)
#endif
iii=iii+1
C Calculate dummy residue coordinates inside the "chain" of a multichain
C system
nres=ires
+c write (iout,*) "dc"
+c do i=1,nres
+c write (iout,'(i5,3f10.5)') i,(dc(j,i),j=1,3)
+c enddo
do i=2,nres-1
c write (iout,*) i,itype(i),itype(i+1),ntyp1,iterter(i)
if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
if (unres_pdb) then
C 2/15/2013 by Adam: corrected insertion of the last dummy residue
- print *,i,'tu dochodze'
+c print *,i,'tu dochodze'
call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
if (fail) then
e2(1)=0.0d0
e2(2)=1.0d0
e2(3)=0.0d0
endif !fail
- print *,i,'a tu?'
+c print *,i,'a tu?'
do j=1,3
c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
enddo
enddo
call flush(iout)
endif
+ zero=.false.
+ do ires=1,nres
+ zero=zero.or.itype(ires).eq.0
+ enddo
+ if (zero) then
+ write (iout,'(2a)') "Gaps in PDB coordinates detected;",
+ & " look for ZERO in the control output above."
+ write (iout,'(2a)') "Repair the PDB file using MODELLER",
+ & " or other softwared and resubmit."
+ call flush(iout)
+ stop
+ endif
c write(iout,*)"before int_from_cart nres",nres
call int_from_cart(.true.,.false.)
do i=1,nres
if (ibeg.eq.0) then
if (unres_pdb) then
do j=1,3
- dc(j,ires)=sccor(j,iii)
+ dc(j,ires_old)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
enddo
endif
C Calculate internal coordinates.
- call int_from_cart(.true.,.true.)
+ call int_from_cart(.true.,out_template_coord)
call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)