subroutine readpdb C Read the PDB file and convert the peptide geometry into virtual-chain C geometry. implicit none include 'DIMENSIONS' include 'COMMON.CONTROL' include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.NAMES' include 'COMMON.SBRIDGE' include 'COMMON.FRAG' character*3 seq,atom,res character*80 card double precision e1(3),e2(3),e3(3) double precision sccor(3,50) integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old double precision dcj integer rescode,kkk,lll,icha,cou,kupa,iprzes logical lsecondary,sccalc,fail,zero integer iterter(maxres) double precision efree_temp iii=0 ibeg=1 ishift1=0 sccalc=.false. bfac=0.0d0 do i=1,maxres iterter(i)=0 enddo ibeg=1 ishift1=0 lsecondary=.false. nhfrag=0 nbfrag=0 iii=0 sccalc=.false. 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. 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) !rc---------------------------------------- !rc to be corrected !!! bfrag(3,nbfrag)=bfrag(1,nbfrag) bfrag(4,nbfrag)=bfrag(2,nbfrag) !rc---------------------------------------- endif 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 c ishift1=ishift1+1 ibeg=2 write (iout,*) "Chain ended",ires,ishift,ires_old,ibeg 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 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. read (card(12:16),*) atom c write (2,'(a)') card c write (iout,*) "ibeg",ibeg c 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 if (ires-ishift+ishift1.ne.ires_old) then ! 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 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_old)=sccor(j,iii) enddo else call sccenter(ires_old,iii,sccor) endif iii=0 sccalc=.true. endif ! Start new residue. c write (iout,*) "ibeg",ibeg 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)=ntyp1 endif ires=ires-ishift+ishift1 ires_old=ires ! 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 !!!!! c ishift1=ishift1-1 !!!!! c write (iout,*) "New chain started",ires,ires_old,ishift, c & ishift1 ires=ires-ishift+ishift1 write (iout,*) "New chain started ires",ires ires_old=ires c ires=ires_old+1 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 ! 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 c write (iout,*) ires,res,(c(j,ires),j=1,3) #ifdef DEBUG write (iout,'(i6,i3,2x,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 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 ! 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 write (iout,'(a,i5)') ' Nres: ',ires c write (iout,*) "iii",iii 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 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 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 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 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) dC(j,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*(-e1(j)+e2(j))/sqrt(2.0d0) 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) dC(j,i)=c(j,i) enddo endif !unres_pdb endif !itype(i+1).eq.ntyp1 endif !itype.eq.ntyp1 enddo write (iout,*) "After loop in readpbd" C Calculate the CM of the last side chain. if (.not. sccalc) then if (unres_pdb) then do j=1,3 dc(j,ires)=sccor(j,iii) enddo else c write (iout,*) "Calling sccenter iii",iii call sccenter(ires,iii,sccor) endif endif 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*(-e1(j)+e2(j))/sqrt(2.0d0) enddo else do j=1,3 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) 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 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)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0) enddo else do j=1,3 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 Calculate internal coordinates. 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,i4,3f8.3,5x,3f8.3)') & restyp(itype(ires)),ires,(c(j,ires),j=1,3), & (c(j,ires+nres),j=1,3) zero=.false. enddo 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 thetaref(i)=theta(i) phiref(i)=phi(i) enddo dc(:,0)=c(:,1) 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 c write (iout,*) i,(dc(j,i),j=1,3),(dc_norm(j,i),j=1,3), c & vbld_inv(i+1) 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 call sc_loc_geom(.false.) call int_from_cart1(.false.) c call chainbuild C Copy the coordinates to reference coordinates do i=1,nres do j=1,3 cref(j,i)=c(j,i) cref(j,i+nres)=c(j,i+nres) enddo enddo 100 format (//' alpha-carbon coordinates ', & ' centroid coordinates'/ 1 ' ', 7X,'X',11X,'Y',11X,'Z', & 10X,'X',11X,'Y',11X,'Z') 110 format (a,'(',i4,')',6f12.5) cc enddiag 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 return end c--------------------------------------------------------------------------- subroutine readpdb_template(k) C Read the PDB file 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.SETUP' integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity 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,iterter(maxres) logical zero do i=1,maxres iterter(i)=0 enddo 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 read (ipdbin,'(a80)',end=10) card 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,*) "! ",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. if (ibeg.eq.0) then if (unres_pdb) then do j=1,3 dc(j,ires_old)=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)=ntyp1 endif ires=ires-ishift+ishift1 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 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 c if (card(27:27).eq."A" .or. card(27:27).eq."B") then c ishift1=ishift1+1 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 ,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 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 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*(-e1(j)+e2(j))/sqrt(2.0d0) 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 (unres_pdb) then do j=1,3 dc(j,ires)=sccor(j,iii) enddo else call sccenter(ires,iii,sccor) endif 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*(-e1(j)+e2(j))/sqrt(2.0d0) enddo else do j=1,3 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) 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 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)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0) enddo else do j=1,3 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 (out_template_coord) 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,i4,3f8.3,5x,3f8.3)') & restyp(itype(ires)),ires,(c(j,ires),j=1,3), & (c(j,ires+nres),j=1,3) enddo 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 Calculate internal coordinates. call int_from_cart(.true.,out_template_coord) call sc_loc_geom(.false.) do i=1,nres thetaref(i)=theta(i) phiref(i)=phi(i) enddo dc(:,0)=c(:,1) 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 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 return end c--------------------------------------------------------------------------- subroutine int_from_cart(lside,lprn) implicit none include 'DIMENSIONS' 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(3,50) 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) c 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.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then write (iout,'(a,i4)') 'Bad Cartesians for residue',i c stop endif vbld(i)=dist(i-1,i) vbld_inv(i)=1.0d0/vbld(i) 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 (itype(1).eq.ntyp1) then c do j=1,3 c c(j,1)=c(j,2)+(c(j,3)-c(j,4)) c enddo c endif c if (itype(nres).eq.ntyp1) then c do j=1,3 c c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3)) c enddo c 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) 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 (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(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(3,50),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 c--------------------------------------------------------------------------- subroutine sc_loc_geom(lprn) 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.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 .and. itype(i).ne.ntyp1) 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 .and. itype(i).ne.ntyp1) 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 c write (iout,*) "x_prime",(x_prime(j),j=1,3) c write (iout,*) "y_prime",(y_prime(j),j=1,3) call vecpr(x_prime,y_prime,z_prime) c write (iout,*) "z_prime",(z_prime(j),j=1,3) 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 write (iout,*) "xxref,yyref,zzref" do i=2,nres iti=itype(i) write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i), & zzref(i) enddo endif return end c--------------------------------------------------------------------------- subroutine bond_regular implicit none include 'DIMENSIONS' include 'COMMON.VAR' 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)=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