X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc-HCD-5D%2Freadpdb-mult.F;h=76cb6b60a680994263d19d0d7ec7765bf389dc5a;hb=915aca0187c1157b991cb5f13960e82e3007cca6;hp=8fd1da8157c2c7441b8937de1b12163eed57ddcd;hpb=05c1789531ec3f44dfebf41b426cb1204329e7ff;p=unres.git diff --git a/source/unres/src-HCD-5D/readpdb-mult.F b/source/unres/src-HCD-5D/readpdb-mult.F index 8fd1da8..76cb6b6 100644 --- a/source/unres/src-HCD-5D/readpdb-mult.F +++ b/source/unres/src-HCD-5D/readpdb-mult.F @@ -19,9 +19,10 @@ C geometry. double precision sccor(3,50) double precision e1(3),e2(3),e3(3) integer rescode,iterter(maxres),cou - logical fail - integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg - double precision dcj + logical fail,sccalc + 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 @@ -31,108 +32,169 @@ C geometry. 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) + 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') then goto 10 else if (card(:3).eq.'TER') then -C End current chain +! End current chain ires_old=ires+2 - itype(ires_old-1)=ntyp1 + 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 + 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 + else call sccenter(ires,iii,sccor) endif + iii=0 + sccalc=.true. endif -C Fish out the ATOM cards. -c if (index(card(1:4),'ATOM').gt.0) then -c read (card(14:16),'(a3)') atom -c if (atom.eq.'CA' .or. atom.eq.'CH3') then -C Calculate the CM of the preceding residue. - read (card(23:26),*) ires - read (card(18:20),'(a3)') res - if (ires-ishift+ishift1.ne.ires_old) then - if (ibeg.eq.0) then - if (unres_pdb) then - do j=1,3 - dc(j,ires+nres)=sccor(j,iii) - enddo +! 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 - call sccenter(ires,iii,sccor) + ishift=ishift-(ires-ishift+ishift1-ires_old-1) + ires=ires-ishift+ishift1 + ires_old=ires endif - endif -C Start new residue. -c write (iout,'(a80)') card - if (ibeg.eq.1) then - ishift=ires-1 - if (res.ne.'GLY' .and. res.ne. 'ACE') then - ishift=ishift-1 - itype(1)=ntyp1 + if (res.eq.'ACE' .or. res.eq.'NHE') then + itype(ires)=10 + else + itype(ires)=rescode(ires,res,0) endif -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 -c write (iout,*) "New chain started",ires,ishift - ibeg=0 - endif - else - ires=ires-ishift -c write (2,*) "ires",ires," ishift",ish - endif - if (atom.eq.'CA' .or. atom.eq.'CH3' .or. - & res.eq.'NHE'.and.atom(:2).eq.'HN') then - if (res.eq.'ACE') then - itype(ires)=10 else - itype(ires)=rescode(ires,res,0) + ires=ires-ishift+ishift1 endif - read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3) - read(card(61:66),*) bfac(ires) -c if(me.eq.king.or..not.out1file) -c & write (iout,'(2i3,2x,a,3f8.3)') -c & ires,itype(ires),res,(c(j,ires),j=1,3) - iii=1 - do j=1,3 - sccor(j,iii)=c(j,ires) - enddo - else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and. - & atom.ne.'N ' .and. atom.ne.'C ') then +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 - read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3) + 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 if(me.eq.king.or..not.out1file) & 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 @@ -142,14 +204,14 @@ 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 - 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 @@ -159,6 +221,7 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue 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 @@ -171,7 +234,7 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue e2(3)=0.0d0 endif do j=1,3 - c(j,i)=c(j,i+1)-1.9d0*e2(j) + c(j,i)=c(j,i+1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0) enddo else !unres_pdb do j=1,3 @@ -179,6 +242,7 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue 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 @@ -186,13 +250,16 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue 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 @@ -251,19 +318,36 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue endif C Calculate internal coordinates. if(me.eq.king.or..not.out1file)then - 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 + 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 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 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) @@ -292,9 +376,9 @@ C Copy the coordinates to reference coordinates enddo 100 format (//' alpha-carbon coordinates ', & ' centroid coordinates'/ - 1 ' ', 6X,'X',11X,'Y',11X,'Z', + 1 ' ', 7X,'X',11X,'Y',11X,'Z', & 10X,'X',11X,'Y',11X,'Z') - 110 format (a,'(',i3,')',6f12.5) + 110 format (a,'(',i4,')',6f12.5) cc enddiag do j=1,nbfrag do i=1,4 @@ -333,8 +417,9 @@ 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) + double precision sccor(3,50) integer rescode,iterter(maxres) + logical zero do i=1,maxres iterter(i)=0 enddo @@ -385,7 +470,7 @@ C Calculate the CM of the preceding residue. 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) @@ -502,7 +587,7 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue e2(3)=0.0d0 endif do j=1,3 - c(j,i)=c(j,i+1)-1.9d0*e2(j) + c(j,i)=c(j,i+1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0) enddo else !unres_pdb do j=1,3 @@ -537,7 +622,7 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue e2(3)=0.0d0 endif do j=1,3 - c(j,nres)=c(j,nres-1)-1.9d0*e2(j) + c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0) enddo else do j=1,3 @@ -569,7 +654,7 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue e2(3)=0.0d0 endif do j=1,3 - c(j,1)=c(j,2)-1.9d0*e2(j) + c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0) enddo else do j=1,3 @@ -590,20 +675,33 @@ 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)" + & "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)') + 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.,.true.) + 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)