subroutine readpdb C Read the PDB file and convert the peptide geometry into virtual-chain C geometry. implicit none include 'DIMENSIONS' include 'DIMENSIONS.ZSCOPT' include 'COMMON.CONTROL' include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.NAMES' character*3 seq,atom,res character*80 card double precision sccor(3,20) integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old double precision dcj integer rescode ibeg=1 ishift1=0 do i=1,10000 read (ipdbin,'(a80)',end=10) 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(14:16),'(a3)') atom if (atom.eq.'CA' .or. atom.eq.'CH3') then C Calculate the CM of the preceding residue. if (ibeg.eq.0) call sccenter(ires,iii,sccor) C Start new residue. ires_old=ires+ishift-ishift1 read (card(23:26),*) ires c print *,"ires_old",ires_old," ires",ires if (card(27:27).eq."A" .or. card(27:27).eq."B") then c ishift1=ishift1+1 endif read (card(18:20),'(a3)') res if (ibeg.eq.1) then ishift=ires-1 if (res.ne.'GLY' .and. res.ne. 'ACE') then ishift=ishift-1 itype(1)=ntyp1 endif ibeg=0 else ishift=ishift+ires-ires_old-1 endif ires=ires-ishift+ishift1 if (res.eq.'ACE') then ity=10 else itype(ires)=rescode(ires,res,0) endif read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3) write (iout,'(2i3,2x,a,3f8.3)') & ires,itype(ires),res,(c(j,ires),j=1,3) iii=1 do j=1,3 sccor(j,iii)=c(j,ires) enddo 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 ') then iii=iii+1 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3) endif endif enddo 10 write (iout,'(a,i5)') ' Nres: ',ires C Calculate the CM of the last side chain. call sccenter(ires,iii,sccor) nres=ires nsup=nres nstart_sup=1 if (itype(nres).ne.10) then nres=nres+1 itype(nres)=ntyp1 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.ntyp1) then nsup=nsup-1 nstart_sup=2 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 C Copy the coordinates to reference coordinates do i=1,2*nres do j=1,3 cref(j,i)=c(j,i) enddo enddo C Calculate internal coordinates. 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,ires+nres),j=1,3) enddo call flush(iout) call int_from_cart(.true.,.true.) do i=1,nres phi_ref(i)=phi(i) theta_ref(i)=theta(i) alph_ref(i)=alph(i) omeg_ref(i)=omeg(i) enddo ishift_pdb=ishift return end c--------------------------------------------------------------------------- subroutine int_from_cart(lside,lprn) implicit none include 'DIMENSIONS' include 'DIMENSIONS.ZSCOPT' include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.NAMES' character*3 seq,atom,res character*80 card double precision sccor(3,20) integer rescode double precision dist,alpha,beta,di integer i,j,iti logical lside,lprn if (lprn) then write (iout,'(/a)') & 'Internal coordinates calculated from crystal structure.' if (lside) then write (iout,'(8a)') ' Res ',' dvb',' Theta', & ' Phi',' Dsc_id',' Dsc',' Alpha', & ' Omega' else write (iout,'(4a)') ' Res ',' dvb',' Theta', & ' Phi' endif endif do i=2,nres iti=itype(i) write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1) if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and. & (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 stop endif 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 if (itype(1).eq.ntyp1) then do j=1,3 c(j,1)=c(j,2)+(c(j,3)-c(j,4)) enddo endif if (itype(nres).eq.ntyp1) then do j=1,3 c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3)) enddo endif if (lside) then do i=2,nres-1 do j=1,3 c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)) enddo iti=itype(i) di=dist(i,nres+i) if (iti.ne.10) then alph(i)=alpha(nres+i,i,maxres2) omeg(i)=beta(nres+i,i,maxres2,i+1) endif if (lprn) & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1), & rad2deg*theta(i),rad2deg*phi(i),dsc(iabs(iti)),di, & rad2deg*alph(i),rad2deg*omeg(i) enddo else if (lprn) then do i=2,nres iti=itype(i) 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 sccenter(ires,nscat,sccor) implicit none include 'DIMENSIONS' include 'COMMON.CHAIN' integer ires,nscat,i,j double precision sccor(3,20),sccmj 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