include 'COMMON.NAMES'
include 'COMMON.CONTROL'
integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
- logical lprn /.false./,fail
+ logical lprn /.false./,fail,sccalc
double precision e1(3),e2(3),e3(3)
double precision dcj,efree_temp
character*3 seq,res
character*5 atom
character*80 card
- double precision sccor(3,20)
+ double precision sccor(3,50)
integer rescode
+ integer iterter(maxres)
efree_temp=0.0d0
ibeg=1
ishift1=0
ires=0
ires_old=0
iii=0
+ sccalc=.false.
lsecondary=.false.
nhfrag=0
nbfrag=0
do
read (ipdbin,'(a80)',end=10) card
-c write (iout,'(a)') card
+! write (iout,'(a)') card
if (card(:5).eq.'HELIX') then
- nhfrag=nhfrag+1
- lsecondary=.true.
- read(card(22:25),*) hfrag(1,nhfrag)
- read(card(34:37),*) hfrag(2,nhfrag)
+ nhfrag=nhfrag+1
+ lsecondary=.true.
+ read(card(22:25),*) hfrag(1,nhfrag)
+ read(card(34:37),*) hfrag(2,nhfrag)
endif
if (card(:5).eq.'SHEET') then
- nbfrag=nbfrag+1
- lsecondary=.true.
- read(card(24:26),*) bfrag(1,nbfrag)
- read(card(35:37),*) bfrag(2,nbfrag)
-crc----------------------------------------
-crc to be corrected !!!
- bfrag(3,nbfrag)=bfrag(1,nbfrag)
- bfrag(4,nbfrag)=bfrag(2,nbfrag)
-crc----------------------------------------
+ nbfrag=nbfrag+1
+ lsecondary=.true.
+ read(card(24:26),*) bfrag(1,nbfrag)
+ read(card(35:37),*) bfrag(2,nbfrag)
+!rc----------------------------------------
+!rc to be corrected !!!
+ bfrag(3,nbfrag)=bfrag(1,nbfrag)
+ bfrag(4,nbfrag)=bfrag(2,nbfrag)
+!rc----------------------------------------
endif
- if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
-c Read free energy
+ if (card(:3).eq.'END') then
+ goto 10
+ else if (card(:3).eq.'TER') then
+! End current chain
+ ires_old=ires+2
+ itype(ires_old-1)=ntyp1
+ iterter(ires_old-1)=1
+ itype(ires_old)=ntyp1
+ iterter(ires_old)=1
+ ishift1=ishift1+1
+ ibeg=2
+! write (iout,*) "Chain ended",ires,ishift,ires_old
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ iii=0
+ sccalc=.true.
+ endif
+! Read free energy
if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
-C Fish out the ATOM cards.
+! Fish out the ATOM cards.
if (index(card(1:4),'ATOM').gt.0) then
+ sccalc=.false.
read (card(12:16),*) atom
-c write (iout,*) "! ",atom," !",ires
-c if (atom.eq.'CA' .or. atom.eq.'CH3') then
+c write (2,'(a)') card
+! write (iout,*) "! ",atom," !",ires
+! if (atom.eq.'CA' .or. atom.eq.'CH3') then
read (card(23:26),*) ires
read (card(18:20),'(a3)') res
-c write (iout,*) "ires",ires,ires-ishift+ishift1,
-c & " ires_old",ires_old
-c write (iout,*) "ishift",ishift," ishift1",ishift1
-c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
+! write (iout,*) "ires",ires,ires-ishift+ishift1,
+! & " ires_old",ires_old
+! write (iout,*) "ishift",ishift," ishift1",ishift1
+! write (iout,*) "IRES",ires-ishift+ishift1,ires_old
if (ires-ishift+ishift1.ne.ires_old) then
-C Calculate the CM of the preceding residue.
-c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+! Calculate the CM of the preceding residue.
+! if (ibeg.eq.0) call sccenter(ires,iii,sccor)
if (ibeg.eq.0) then
-c write (iout,*) "Calculating sidechain center iii",iii
+! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires)=sccor(j,iii)
+ dc(j,ires+nres)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
endif
iii=0
+ sccalc=.true.
endif
-C Start new residue.
+! Start new residue.
if (res.eq.'Cl-' .or. res.eq.'Na+') then
ires=ires_old
cycle
endif
ires=ires-ishift+ishift1
ires_old=ires
-c write (iout,*) "ishift",ishift," ires",ires,
-c & " ires_old",ires_old
- ibeg=0
+! write (iout,*) "ishift",ishift," ires",ires,&
+! " ires_old",ires_old
+ ibeg=0
+ else if (ibeg.eq.2) then
+! Start a new chain
+ ishift=-ires_old+ires-1 !!!!!
+ ishift1=ishift1-1 !!!!!
+! write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+ ires=ires-ishift+ishift1
+ ires_old=ires
+ ibeg=0
else
ishift=ishift-(ires-ishift+ishift1-ires_old-1)
ires=ires-ishift+ishift1
else
ires=ires-ishift+ishift1
endif
-c write (iout,*) "ires_old",ires_old," ires",ires
+! write (iout,*) "ires_old",ires_old," ires",ires
if (card(27:27).eq."A" .or. card(27:27).eq."B") then
-c ishift1=ishift1+1
+! ishift1=ishift1+1
endif
-c write (2,*) "ires",ires," res ",res," ity",ity
+! write (2,*) "ires",ires," res ",res!," ity"!,ity
if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
& res.eq.'NHE'.and.atom(:2).eq.'HN') then
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
-c write (iout,*) "backbone ",atom
+! write (iout,*) "backbone ",atom
#ifdef DEBUG
write (iout,'(2i3,2x,a,3f8.3)')
& ires,itype(ires),res,(c(j,ires),j=1,3)
do j=1,3
sccor(j,iii)=c(j,ires)
enddo
- if (ishift.ne.0) then
- ires_ca=ires+ishift-ishift1
- else
- ires_ca=ires
- endif
-c write (*,*) card(23:27),ires,itype(ires)
- else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
- & atom.ne.'N' .and. atom.ne.'C' .and.
- & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
+c write (2,*) card(23:27),ires,itype(ires),iii
+ else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
+ & atom.ne.'N' .and. atom.ne.'C' .and.
+ & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
& atom.ne.'OXT' .and. atom(:2).ne.'3H') then
-c write (iout,*) "sidechain ",atom
+! write (iout,*) "sidechain ",atom
iii=iii+1
read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+c write (2,*) "iii",iii
endif
endif
enddo
- 10 continue
-#ifdef DEBUG
- write (iout,'(a,i5)') ' Number of residues found: ',ires
-#endif
- if (ires.eq.0) return
-C Calculate the CM of the last side chain.
- if (iii.gt.0) then
- if (unres_pdb) then
- do j=1,3
- dc(j,ires)=sccor(j,iii)
- enddo
- else
- call sccenter(ires,iii,sccor)
- endif
- endif
+ 10 write (iout,'(a,i5)') ' Nres: ',ires
+C Calculate dummy residue coordinates inside the "chain" of a multichain
+C system
nres=ires
+ do i=2,nres-1
+c write (iout,*) i,itype(i)
+
+ if (itype(i).eq.ntyp1) then
+ 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.
+ if (.not.sccalc) call sccenter(ires,iii,sccor)
nsup=nres
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
itype(nres)=ntyp1
- if (unres_pdb) then
-C 2/15/2013 by Adam: corrected insertion of the last dummy residue
- call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
- if (fail) then
- e2(1)=0.0d0
- e2(2)=1.0d0
- e2(3)=0.0d0
- endif
- do j=1,3
- c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
- enddo
- else
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
- endif
endif
do i=2,nres-1
do j=1,3
if (itype(1).eq.ntyp1) then
nsup=nsup-1
nstart_sup=2
- if (unres_pdb) then
-C 2/15/2013 by Adam: corrected insertion of the first dummy residue
- call refsys(2,3,4,e1,e2,e3,fail)
- if (fail) then
- e2(1)=0.0d0
- e2(2)=1.0d0
- e2(3)=0.0d0
- endif
- do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
- enddo
- else
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
- endif
endif
-C Copy the coordinates to reference coordinates
-c do i=1,2*nres
-c do j=1,3
-c cref(j,i)=c(j,i)
-c enddo
-c enddo
C Calculate internal coordinates.
if (lprn) then
write (iout,'(/a)')
character*3 seq,res
c character*5 atom
character*80 card
- dimension sccor(3,20)
+ dimension sccor(3,50)
integer rescode
logical lside,lprn
if (lprn) then
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'COMMON.CHAIN'
- dimension sccor(3,20)
+ dimension sccor(3,50)
do j=1,3
sccmj=0.0D0
do i=1,nscat
end
c---------------------------------------------------------------------------
subroutine bond_regular
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
+ implicit none
+ include 'DIMENSIONS'
include 'COMMON.VAR'
- include 'COMMON.LOCAL'
- include 'COMMON.CALC'
+ include 'COMMON.LOCAL'
include 'COMMON.INTERACT'
include 'COMMON.CHAIN'
+ integer i,i1,i2
do i=1,nres-1
vbld(i+1)=vbl
- vbld_inv(i+1)=1.0d0/vbld(i+1)
- vbld(i+1+nres)=dsc(itype(i+1))
- vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
+ vbld_inv(i+1)=vblinv
+ vbld(i+1+nres)=dsc(iabs(itype(i+1)))
+ vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
c print *,vbld(i+1),vbld(i+1+nres)
enddo
+c Adam 2/26/20 Alter virtual bonds for non-blocking end groups of each chain
+ do i=1,nchain
+ i1=chain_border(1,i)
+ i2=chain_border(2,i)
+ if (i1.gt.1) then
+ vbld(i1)=vbld(i1)/2
+ vbld_inv(i1)=vbld_inv(i1)*2
+ endif
+ if (i2.lt.nres) then
+ vbld(i2+1)=vbld(i2+1)/2
+ vbld_inv(i2+1)=vbld_inv(i2+1)*2
+ endif
+ enddo
return
end
+c---------------------------------------------------------------------------
subroutine readpdb_template(k)
C Read the PDB file with gaps for read_constr_homology with read2sigma
C and convert the peptide geometry into virtual-chain geometry.
character*3 seq,res
character*5 atom
character*80 card
- double precision sccor(3,20)
- integer rescode
- efree_temp=0.0d0
+ double precision sccor(3,50)
+ integer rescode,iterter(maxres)
+ do i=1,maxres
+ iterter(i)=0
+ enddo
ibeg=1
ishift1=0
ishift=0
lsecondary=.false.
nhfrag=0
nbfrag=0
- do
+ do
read (ipdbin,'(a80)',end=10) card
-c write (iout,'(a)') card
- if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
+ if (card(:3).eq.'END') then
+ goto 10
+ else if (card(:3).eq.'TER') then
+C End current chain
+ ires_old=ires+2
+ itype(ires_old-1)=ntyp1
+ iterter(ires_old-1)=1
+ itype(ires_old)=ntyp1
+ iterter(ires_old)=1
+ ibeg=2
+c write (iout,*) "Chain ended",ires,ishift,ires_old
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ endif
C Fish out the ATOM cards.
if (index(card(1:4),'ATOM').gt.0) then
read (card(12:16),*) atom
c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
if (ires-ishift+ishift1.ne.ires_old) then
C Calculate the CM of the preceding residue.
-c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
if (ibeg.eq.0) then
-c write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
dc(j,ires)=sccor(j,iii)
ires_old=ires
c write (iout,*) "ishift",ishift," ires",ires,
c & " ires_old",ires_old
+c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
+ ibeg=0
+ else if (ibeg.eq.2) then
+c Start a new chain
+ ishift=-ires_old+ires-1
+ ires=ires_old+1
+c write (iout,*) "New chain started",ires,ishift
ibeg=0
else
ishift=ishift-(ires-ishift+ishift1-ires_old-1)
ires=ires-ishift+ishift1
endif
c write (iout,*) "ires_old",ires_old," ires",ires
- if (card(27:27).eq."A" .or. card(27:27).eq."B") then
+c if (card(27:27).eq."A" .or. card(27:27).eq."B") then
c ishift1=ishift1+1
- endif
+c endif
c write (2,*) "ires",ires," res ",res," ity",ity
if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
& res.eq.'NHE'.and.atom(:2).eq.'HN') then
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
-c write (iout,*) "backbone ",atom
+c write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
#ifdef DEBUG
write (iout,'(2i3,2x,a,3f8.3)')
& ires,itype(ires),res,(c(j,ires),j=1,3)
endif
endif
enddo
- 10 continue
-#ifdef DEBUG
- write (iout,'(a,i5)') ' Number of residues found: ',ires
-#endif
- if (ires.eq.0) return
+ 10 write (iout,'(a,i5)') ' Nres: ',ires
+C Calculate dummy residue coordinates inside the "chain" of a multichain
+C system
+ nres=ires
+ do i=2,nres-1
+c write (iout,*) i,itype(i),itype(i+1)
+ if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
+ if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) 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
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ 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
+ do j=1,3
+ c(j,i)=c(j,i-1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i-2)-c(j,i-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i-1)+dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ else !itype(i+1).eq.ntyp1
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,i)=c(j,i+1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i+3)-c(j,i+2))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i+1)-dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ endif !itype(i+1).eq.ntyp1
+ endif !itype.eq.ntyp1
+ enddo
C Calculate the CM of the last side chain.
- if (iii.gt.0) then
if (unres_pdb) then
do j=1,3
dc(j,ires)=sccor(j,iii)
else
call sccenter(ires,iii,sccor)
endif
- endif
- nres=ires
nsup=nres
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
itype(nres)=ntyp1
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
+ enddo
+ else
do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
endif
+ endif
do i=2,nres-1
do j=1,3
c(j,i+nres)=dc(j,i)
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
+ c(j,1)=c(j,2)-1.9d0*e2(j)
enddo
else
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
c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
c & vbld_inv(i+nres)
enddo
-c call chainbuild
-C Copy the coordinates to reference coordinates
- do i=1,2*nres
+ do i=1,nres
do j=1,3
cref(j,i)=c(j,i)
+ cref(j,i+nres)=c(j,i+nres)
+ enddo
+ enddo
+ do i=1,2*nres
+ do j=1,3
chomo(j,i,k)=c(j,i)
enddo
enddo
-
- ishift_pdb=ishift
return
end
projects / unres.git / blobdiff