X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Freadpdb.F;h=ef48c2a2bb9cc74fcd3faa5bd804b46e6d831f6f;hb=5e2358117d5efe154a9c192de01e50c1f84f6a43;hp=8b6f3313013b7cbd4d6b8de16b44c01aecce859f;hpb=a09fdb5f3686a0c1242c8dd3b6dfadf0d3678aaf;p=unres.git diff --git a/source/unres/src_MD-M/readpdb.F b/source/unres/src_MD-M/readpdb.F index 8b6f331..ef48c2a 100644 --- a/source/unres/src_MD-M/readpdb.F +++ b/source/unres/src_MD-M/readpdb.F @@ -13,18 +13,31 @@ C geometry. include 'COMMON.CONTROL' include 'COMMON.DISTFIT' include 'COMMON.SETUP' - character*3 seq,atom,res - character*80 card - dimension sccor(3,20) + integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity, + & ishift_pdb + logical lprn /.true./,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 - logical fail + efree_temp=0.0d0 ibeg=1 + ishift1=0 + ishift=0 +c write (2,*) "UNRES_PDB",unres_pdb + ires=0 + ires_old=0 + nres=0 + iii=0 lsecondary=.false. nhfrag=0 nbfrag=0 - do + do i=1,100000 read (ipdbin,'(a80)',end=10) card +c write (iout,'(a)') card if (card(:5).eq.'HELIX') then nhfrag=nhfrag+1 lsecondary=.true. @@ -46,80 +59,120 @@ crc---------------------------------------- goto 10 else if (card(:3).eq.'TER') then C End current chain - ires_old=ires+1 - itype(ires_old)=21 + ires_old=ires+1 + ishift1=ishift1+1 + itype(ires_old)=ntyp1 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 + else call sccenter(ires,iii,sccor) endif + iii=0 endif +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(14:16),'(a3)') atom - if (atom.eq.'CA' .or. atom.eq.'CH3') 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+nres)=sccor(j,iii) enddo else - call sccenter(ires,iii,sccor) + call sccenter(ires_old,iii,sccor) endif + iii=0 endif C Start new residue. -c write (iout,'(a80)') card - read (card(24:26),*) ires - read (card(18:20),'(a3)') res - if (ibeg.eq.1) then + 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 + itype(1)=ntyp1 endif -c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift - ibeg=0 + ires=ires-ishift+ishift1 + ires_old=ires +c write (iout,*) "ishift",ishift," ires",ires, +c & " ires_old",ires_old + 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 +c ishift=-ires_old+ires-1 +c ishift1=ishift1+1 +c 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 + ires_old=ires endif - ires=ires-ishift -c write (2,*) "ires",ires," ishift",ishift - if (res.eq.'ACE') then - ity=10 + 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) - if(me.eq.king.or..not.out1file) - & write (iout,'(2i3,2x,a,3f8.3)') - & ires,itype(ires),res,(c(j,ires),j=1,3) - iii=1 +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 - else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and. - & atom.ne.'N ' .and. atom.ne.'C ') then +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 if(me.eq.king.or..not.out1file) - & write (iout,'(a,i5)') ' Nres: ',ires + 10 write (iout,'(a,i5)') ' Number of residues found: ',ires + if (ires.eq.0) return 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.21) then + if (itype(i).eq.ntyp1) then c write (iout,*) "dummy",i,itype(i) do j=1,3 c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2 @@ -129,18 +182,21 @@ c c(j,i)=(c(j,i-1)+c(j,i+1))/2 endif 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) enddo - else + else call sccenter(ires,iii,sccor) endif + endif +c nres=ires nsup=nres nstart_sup=1 if (itype(nres).ne.10) then nres=nres+1 - itype(nres)=21 + 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) @@ -169,7 +225,7 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue c(j,nres+1)=c(j,1) c(j,2*nres)=c(j,nres) enddo - if (itype(1).eq.21) then + if (itype(1).eq.ntyp1) then nsup=nsup-1 nstart_sup=2 if (unres_pdb) then @@ -191,8 +247,28 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue 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), @@ -201,6 +277,7 @@ C Calculate internal coordinates. endif call int_from_cart(.true.,.false.) call sc_loc_geom(.true.) +c wczesbiej bylo false do i=1,nres thetaref(i)=theta(i) phiref(i)=phi(i) @@ -222,6 +299,13 @@ c & vbld_inv(i+nres) c call chainbuild C Copy the coordinates to reference coordinates C Splits to single chain if occurs + +c do i=1,2*nres +c do j=1,3 +c cref(j,i,cou)=c(j,i) +c enddo +c enddo +c kkk=1 lll=0 cou=1 @@ -229,7 +313,7 @@ C Splits to single chain if occurs lll=lll+1 cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3) if (i.gt.1) then - if ((itype(i-1).eq.21)) then + if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then chain_length=lll-1 kkk=kkk+1 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3) @@ -245,6 +329,8 @@ c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3) endif enddo enddo + write (iout,*) chain_length + if (chain_length.eq.0) chain_length=nres do j=1,3 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1) chain_rep(j,chain_length+nres,symetr) @@ -257,10 +343,10 @@ c do kkk=1,chain_length c write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3) c enddo c enddo -c enddiagnostic +c enddiagnostic C makes copy of chains write (iout,*) "symetr", symetr - + if (symetr.gt.1) then call permut(symetr) nperm=1 @@ -306,7 +392,7 @@ c diag 1 ' ', 6X,'X',11X,'Y',11X,'Z', & 10X,'X',11X,'Y',11X,'Z') 110 format (a,'(',i3,')',6f12.5) - + enddo cc enddiag do j=1,nbfrag @@ -320,7 +406,7 @@ cc enddiag hfrag(i,j)=hfrag(i,j)-ishift enddo enddo - + ishift_pdb=ishift return end c--------------------------------------------------------------------------- @@ -329,7 +415,7 @@ c--------------------------------------------------------------------------- include 'DIMENSIONS' #ifdef MPI include "mpif.h" -#endif +#endif include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' @@ -339,33 +425,29 @@ c--------------------------------------------------------------------------- include 'COMMON.NAMES' include 'COMMON.CONTROL' include 'COMMON.SETUP' - character*3 seq,atom,res + character*3 seq,res +c character*5 atom character*80 card dimension sccor(3,20) integer rescode logical lside,lprn -#ifdef MPI if(me.eq.king.or..not.out1file)then -#endif 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' + & ' Gamma',' Dsc_id',' Dsc',' Alpha', + & ' Beta ' else write (iout,'(4a)') ' Res ',' dvb',' Theta', - & ' Phi' + & ' Gamma' endif endif -#ifdef MPI endif -#endif do i=1,nres-1 iti=itype(i) - if (iti.ne.21 .and. itype(i+1).ne.21 .and. - & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then + 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 @@ -396,6 +478,9 @@ c endif 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.ntyp1. 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 @@ -429,7 +514,7 @@ c------------------------------------------------------------------------------- include 'DIMENSIONS' #ifdef MPI include "mpif.h" -#endif +#endif include 'COMMON.LOCAL' include 'COMMON.VAR' include 'COMMON.CHAIN' @@ -447,7 +532,7 @@ c------------------------------------------------------------------------------- enddo enddo do i=2,nres-1 - if (itype(i).ne.10 .and. itype(i).ne.21) then + 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 @@ -467,7 +552,7 @@ c------------------------------------------------------------------------------- sinfac2=0.5d0/(1.0d0-costtab(i+1)) sinfac=dsqrt(sinfac2) it=itype(i) - if (it.ne.10 .and. itype(i).ne.21) then + 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 @@ -507,14 +592,9 @@ c if (lprn) then do i=2,nres iti=itype(i) -#ifdef MPI if(me.eq.king.or..not.out1file) & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i), & yyref(i),zzref(i) -#else - write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i), - & zzref(i) -#endif enddo endif return @@ -552,4 +632,3 @@ c print *,vbld(i+1),vbld(i+1+nres) enddo return end -