subroutine readpdb C Read the PDB file and convert the peptide geometry into virtual-chain C geometry. implicit real*8 (a-h,o-z) include 'DIMENSIONS' include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.NAMES' include 'COMMON.CONTROL' include 'COMMON.DISTFIT' include 'COMMON.SETUP' integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity, & ishift_pdb logical lprn /.false./,fail 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) integer rescode efree_temp=0.0d0 ibeg=1 ishift1=0 ishift=0 c write (2,*) "UNRES_PDB",unres_pdb ires=0 ires_old=0 iii=0 lsecondary=.false. nhfrag=0 nbfrag=0 do i=1,10000 read (ipdbin,'(a80)',end=10) card c 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) 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---------------------------------------- endif if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10 c Read free energy if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp C Fish out the ATOM cards. if (index(card(1:4),'ATOM').gt.0) then read (card(12:16),*) atom c write (iout,*) "! ",atom," !",ires c 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 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) enddo else call sccenter(ires_old,iii,sccor) endif iii=0 endif C Start new residue. if (res.eq.'Cl-' .or. res.eq.'Na+') then ires=ires_old cycle else if (ibeg.eq.1) then c write (iout,*) "BEG ires",ires ishift=ires-1 if (res.ne.'GLY' .and. res.ne. 'ACE') then ishift=ishift-1 itype(1)=21 endif ires=ires-ishift+ishift1 ires_old=ires c write (iout,*) "ishift",ishift," ires",ires, c & " ires_old",ires_old ibeg=0 else ishift=ishift-(ires-ishift+ishift1-ires_old-1) ires=ires-ishift+ishift1 ires_old=ires endif if (res.eq.'ACE' .or. res.eq.'NHE') then itype(ires)=10 else itype(ires)=rescode(ires,res,0) endif else 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 ishift1=ishift1+1 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 #ifdef DEBUG write (iout,'(2i3,2x,a,3f8.3)') & ires,itype(ires),res,(c(j,ires),j=1,3) #endif iii=iii+1 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. & atom.ne.'OXT' .and. atom(:2).ne.'3H') then c write (iout,*) "sidechain ",atom iii=iii+1 read(card(31:54),'(3f8.3)') (sccor(j,iii),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 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 nres=ires nsup=nres nstart_sup=1 if (itype(nres).ne.10) then nres=nres+1 itype(nres)=21 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) 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) enddo enddo do j=1,3 c(j,nres+1)=c(j,1) c(j,2*nres)=c(j,nres) enddo if (itype(1).eq.21) 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) 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)') & "Cartesian coordinates of the reference structure" write (iout,'(a,3(3x,a5),5x,3(3x,a5))') & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)" do ires=1,nres write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)') & restyp(itype(ires)),ires,(c(j,ires),j=1,3), & (c(j,ires+nres),j=1,3) enddo endif C Calculate internal coordinates. if(me.eq.king.or..not.out1file)then write (iout,'(a)') & "Backbone and SC coordinates as read from the PDB" do ires=1,nres write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3), & (c(j,nres+ires),j=1,3) enddo endif call int_from_cart(.true.,.false.) call sc_loc_geom(.false.) do i=1,nres thetaref(i)=theta(i) phiref(i)=phi(i) enddo do i=1,nres-1 do j=1,3 dc(j,i)=c(j,i+1)-c(j,i) dc_norm(j,i)=dc(j,i)*vbld_inv(i+1) enddo enddo do i=2,nres-1 do j=1,3 dc(j,i+nres)=c(j,i+nres)-c(j,i) dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres) 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 j=1,3 cref(j,i)=c(j,i) enddo enddo do j=1,nbfrag do i=1,4 bfrag(i,j)=bfrag(i,j)-ishift enddo enddo do j=1,nhfrag do i=1,2 hfrag(i,j)=hfrag(i,j)-ishift enddo enddo ishift_pdb=ishift return end c--------------------------------------------------------------------------- subroutine int_from_cart(lside,lprn) implicit real*8 (a-h,o-z) include 'DIMENSIONS' #ifdef MPI include "mpif.h" #endif include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.NAMES' include 'COMMON.CONTROL' include 'COMMON.SETUP' character*3 seq,res c character*5 atom character*80 card dimension sccor(3,20) integer rescode logical lside,lprn if(me.eq.king.or..not.out1file)then if (lprn) then write (iout,'(/a)') & 'Internal coordinates calculated from crystal structure.' if (lside) then write (iout,'(8a)') ' Res ',' dvb',' Theta', & ' Gamma',' Dsc_id',' Dsc',' Alpha', & ' Beta ' else write (iout,'(4a)') ' Res ',' dvb',' Theta', & ' Gamma' endif endif endif do i=1,nres-1 iti=itype(i) if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then write (iout,'(a,i4)') 'Bad Cartesians for residue',i ctest stop endif vbld(i+1)=dist(i,i+1) vbld_inv(i+1)=1.0d0/vbld(i+1) if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1) if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1) enddo c if (unres_pdb) then c if (itype(1).eq.21) then c theta(3)=90.0d0*deg2rad c phi(4)=180.0d0*deg2rad c vbld(2)=3.8d0 c vbld_inv(2)=1.0d0/vbld(2) c endif c if (itype(nres).eq.21) then c theta(nres)=90.0d0*deg2rad c phi(nres)=180.0d0*deg2rad c vbld(nres)=3.8d0 c vbld_inv(nres)=1.0d0/vbld(2) c endif c endif if (lside) then do i=2,nres-1 do j=1,3 c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) & +(c(j,i+1)-c(j,i))*vbld_inv(i+1)) enddo iti=itype(i) di=dist(i,nres+i) C 10/03/12 Adam: Correction for zero SC-SC bond length if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0) & di=dsc(itype(i)) vbld(i+nres)=di if (itype(i).ne.10) then vbld_inv(i+nres)=1.0d0/di else vbld_inv(i+nres)=0.0d0 endif if (iti.ne.10) then alph(i)=alpha(nres+i,i,maxres2) omeg(i)=beta(nres+i,i,maxres2,i+1) endif if(me.eq.king.or..not.out1file)then if (lprn) & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i), & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i), & rad2deg*alph(i),rad2deg*omeg(i) endif enddo else if (lprn) then do i=2,nres iti=itype(i) if(me.eq.king.or..not.out1file) & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1), & rad2deg*theta(i),rad2deg*phi(i) enddo endif return end c------------------------------------------------------------------------------- subroutine sc_loc_geom(lprn) implicit real*8 (a-h,o-z) include 'DIMENSIONS' #ifdef MPI include "mpif.h" #endif include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.NAMES' include 'COMMON.CONTROL' include 'COMMON.SETUP' double precision x_prime(3),y_prime(3),z_prime(3) logical lprn do i=1,nres-1 do j=1,3 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i)) enddo enddo do i=2,nres-1 if (itype(i).ne.10) then do j=1,3 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i)) enddo else do j=1,3 dc_norm(j,i+nres)=0.0d0 enddo endif enddo do i=2,nres-1 costtab(i+1) =dcos(theta(i+1)) sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1)) cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1))) sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1))) cosfac2=0.5d0/(1.0d0+costtab(i+1)) cosfac=dsqrt(cosfac2) sinfac2=0.5d0/(1.0d0-costtab(i+1)) sinfac=dsqrt(sinfac2) it=itype(i) if (it.ne.10) then c C Compute the axes of tghe local cartesian coordinates system; store in c x_prime, y_prime and z_prime c do j=1,3 x_prime(j) = 0.00 y_prime(j) = 0.00 z_prime(j) = 0.00 enddo do j = 1,3 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac enddo call vecpr(x_prime,y_prime,z_prime) c C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i), C to local coordinate system. Store in xx, yy, zz. c xx=0.0d0 yy=0.0d0 zz=0.0d0 do j = 1,3 xx = xx + x_prime(j)*dc_norm(j,i+nres) yy = yy + y_prime(j)*dc_norm(j,i+nres) zz = zz + z_prime(j)*dc_norm(j,i+nres) enddo xxref(i)=xx yyref(i)=yy zzref(i)=zz else xxref(i)=0.0d0 yyref(i)=0.0d0 zzref(i)=0.0d0 endif enddo if (lprn) then do i=2,nres iti=itype(i) if(me.eq.king.or..not.out1file) & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i), & yyref(i),zzref(i) enddo endif return end c--------------------------------------------------------------------------- subroutine sccenter(ires,nscat,sccor) implicit real*8 (a-h,o-z) include 'DIMENSIONS' include 'COMMON.CHAIN' dimension sccor(3,20) do j=1,3 sccmj=0.0D0 do i=1,nscat sccmj=sccmj+sccor(j,i) enddo dc(j,ires)=sccmj/nscat enddo return end c--------------------------------------------------------------------------- subroutine bond_regular implicit real*8 (a-h,o-z) include 'DIMENSIONS' include 'COMMON.VAR' include 'COMMON.LOCAL' include 'COMMON.CALC' include 'COMMON.INTERACT' include 'COMMON.CHAIN' 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)) c print *,vbld(i+1),vbld(i+1+nres) enddo return end 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. implicit real*8 (a-h,o-z) include 'DIMENSIONS' include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.NAMES' include 'COMMON.CONTROL' include 'COMMON.DISTFIT' include 'COMMON.SETUP' include 'COMMON.MD' integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity, & ishift_pdb logical lprn /.false./,fail 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) integer rescode efree_temp=0.0d0 ibeg=1 ishift1=0 ishift=0 c write (2,*) "UNRES_PDB",unres_pdb ires=0 ires_old=0 iii=0 lsecondary=.false. nhfrag=0 nbfrag=0 do i=1,10000 read (ipdbin,'(a80)',end=10) card c write (iout,'(a)') card if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10 C Fish out the ATOM cards. if (index(card(1:4),'ATOM').gt.0) then read (card(12:16),*) atom c write (iout,*) "! ",atom," !",ires c 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 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) enddo else call sccenter(ires_old,iii,sccor) endif iii=0 endif C Start new residue. if (res.eq.'Cl-' .or. res.eq.'Na+') then ires=ires_old cycle else if (ibeg.eq.1) then c write (iout,*) "BEG ires",ires ishift=ires-1 if (res.ne.'GLY' .and. res.ne. 'ACE') then ishift=ishift-1 itype(1)=21 endif ires=ires-ishift+ishift1 ires_old=ires c write (iout,*) "ishift",ishift," ires",ires, c & " ires_old",ires_old ibeg=0 else ishift=ishift-(ires-ishift+ishift1-ires_old-1) ires=ires-ishift+ishift1 ires_old=ires endif if (res.eq.'ACE' .or. res.eq.'NHE') then itype(ires)=10 else itype(ires)=rescode(ires,res,0) endif else 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 ishift1=ishift1+1 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 #ifdef DEBUG write (iout,'(2i3,2x,a,3f8.3)') & ires,itype(ires),res,(c(j,ires),j=1,3) #endif iii=iii+1 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. & atom.ne.'OXT' .and. atom(:2).ne.'3H') then c write (iout,*) "sidechain ",atom iii=iii+1 read(card(31:54),'(3f8.3)') (sccor(j,iii),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 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 nres=ires nsup=nres nstart_sup=1 if (itype(nres).ne.10) then nres=nres+1 itype(nres)=21 do j=1,3 dcj=c(j,nres-2)-c(j,nres-3) c(j,nres)=c(j,nres-1)+dcj c(j,2*nres)=c(j,nres) enddo endif do i=2,nres-1 do j=1,3 c(j,i+nres)=dc(j,i) enddo enddo do j=1,3 c(j,nres+1)=c(j,1) c(j,2*nres)=c(j,nres) enddo if (itype(1).eq.21) 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) c(j,1)=c(j,2)-dcj c(j,nres+1)=c(j,1) enddo endif endif C Calculate internal coordinates. if (lprn) then write (iout,'(/a)') & "Cartesian coordinates of the reference structure" write (iout,'(a,3(3x,a5),5x,3(3x,a5))') & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)" do ires=1,nres write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)') & restyp(itype(ires)),ires,(c(j,ires),j=1,3), & (c(j,ires+nres),j=1,3) enddo endif C Calculate internal coordinates. if(me.eq.king.or..not.out1file)then write (iout,'(a)') & "Backbone and SC coordinates as read from the PDB" do ires=1,nres write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3), & (c(j,nres+ires),j=1,3) enddo endif call int_from_cart(.true.,.false.) call sc_loc_geom(.false.) do i=1,nres thetaref(i)=theta(i) phiref(i)=phi(i) enddo do i=1,nres-1 do j=1,3 dc(j,i)=c(j,i+1)-c(j,i) dc_norm(j,i)=dc(j,i)*vbld_inv(i+1) enddo enddo do i=2,nres-1 do j=1,3 dc(j,i+nres)=c(j,i+nres)-c(j,i) dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres) 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 j=1,3 cref(j,i)=c(j,i) chomo(j,i,k)=c(j,i) enddo enddo ishift_pdb=ishift return end