X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Freadpdb.F;h=7aa8fd41b9d593a5b850536c668bbcb9568f9252;hb=dc7deba07f8e1f5bc5eb8e6e2fb433c3636c7782;hp=edd478e8ec4327cc3924807f4de8abcbf688cf72;hpb=478a9d9a1c99eb3f4bc4ca676ff3162bdd01d633;p=unres.git diff --git a/source/unres/src_MD-M/readpdb.F b/source/unres/src_MD-M/readpdb.F index edd478e..7aa8fd4 100644 --- a/source/unres/src_MD-M/readpdb.F +++ b/source/unres/src_MD-M/readpdb.F @@ -16,7 +16,12 @@ C geometry. character*3 seq,atom,res character*80 card dimension sccor(3,20) - integer rescode + double precision e1(3),e2(3),e3(3) + integer rescode,iterter(maxres),cou + logical fail + do i=1,maxres + iterter(i)=0 + enddo ibeg=1 lsecondary=.false. nhfrag=0 @@ -44,10 +49,13 @@ 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+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 + write (iout,*) "Chain ended",ires,ishift,ires_old if (unres_pdb) then do j=1,3 dc(j,ires)=sccor(j,iii) @@ -72,13 +80,13 @@ C Calculate the CM of the preceding residue. endif C Start new residue. c write (iout,'(a80)') card - read (card(24:26),*) ires + read (card(23:26),*) ires 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)=21 + itype(1)=ntyp1 endif c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift ibeg=0 @@ -91,7 +99,7 @@ c write (iout,*) "New chain started",ires,ishift ires=ires-ishift c write (2,*) "ires",ires," ishift",ishift if (res.eq.'ACE') then - ity=10 + itype(ires)=10 else itype(ires)=rescode(ires,res,0) endif @@ -116,15 +124,55 @@ 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 -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 -c c(j,i)=(c(j,i-1)+c(j,i+1))/2 - dc(j,i)=c(j,i) - enddo - endif + 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 + 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?' + 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*e2(j) + 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 @@ -138,14 +186,22 @@ C Calculate the CM of the last side chain. nstart_sup=1 if (itype(nres).ne.10) then nres=nres+1 - itype(nres)=21 + itype(nres)=ntyp1 if (unres_pdb) then - c(1,nres)=c(1,nres-1)+3.8d0 - c(2,nres)=c(2,nres-1) - c(3,nres)=c(3,nres-1) +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*e2(j) + enddo else do j=1,3 - dcj=c(j,nres-2)-c(j,nres-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 @@ -160,16 +216,23 @@ C Calculate the CM of the last side chain. 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 - c(1,1)=c(1,2)-3.8d0 - c(2,1)=c(2,2) - c(3,1)=c(3,2) +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*e2(j) + enddo else do j=1,3 - dcj=c(j,4)-c(j,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 @@ -183,6 +246,7 @@ C Calculate internal coordinates. & (c(j,nres+ires),j=1,3) enddo endif +C print *,"before int_from_cart" call int_from_cart(.true.,.false.) call sc_loc_geom(.true.) do i=1,nres @@ -213,7 +277,7 @@ 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) @@ -229,6 +293,8 @@ 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) @@ -304,7 +370,6 @@ cc enddiag hfrag(i,j)=hfrag(i,j)-ishift enddo enddo - return end c--------------------------------------------------------------------------- @@ -348,7 +413,7 @@ c--------------------------------------------------------------------------- #endif do i=1,nres-1 iti=itype(i) - if (iti.ne.21 .and. itype(i+1).ne.21 .and. + if (iti.ne.ntyp1 .and. itype(i+1).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 ctest stop @@ -372,6 +437,7 @@ c vbld(nres)=3.8d0 c vbld_inv(nres)=1.0d0/vbld(2) c endif c endif + print *,"A TU2" if (lside) then do i=2,nres-1 do j=1,3 @@ -431,7 +497,7 @@ c------------------------------------------------------------------------------- enddo enddo do i=2,nres-1 - if (itype(i).ne.10 .and. itype(i).ne.21) then + if (itype(i).ne.10 .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 @@ -451,7 +517,7 @@ 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 .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 @@ -530,8 +596,8 @@ c--------------------------------------------------------------------------- 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)) + 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 return