X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fcluster%2Fwham%2Fsrc-HCD%2Freadpdb.F;h=98e538e16a9ab52f427d66d282d0fd8f63c64112;hb=0b41c0eed4b401e3554fac2830d4234f83abdd98;hp=2e7360184568a875de3c3c66b4f998268bf5c969;hpb=de4daf245936d67b5c08eb584fca985adab9928e;p=unres.git diff --git a/source/cluster/wham/src-HCD/readpdb.F b/source/cluster/wham/src-HCD/readpdb.F index 2e73601..98e538e 100644 --- a/source/cluster/wham/src-HCD/readpdb.F +++ b/source/cluster/wham/src-HCD/readpdb.F @@ -21,6 +21,7 @@ C geometry. character*80 card double precision sccor(3,20) integer rescode + integer iterter(maxres) efree_temp=0.0d0 ibeg=1 ishift1=0 @@ -34,53 +35,73 @@ c write (2,*) "UNRES_PDB",unres_pdb nbfrag=0 do read (ipdbin,'(a80)',end=10) card -c write (iout,'(a)') card +! write (iout,'(a)') card 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' .or. card(:3).eq.'TER') goto 10 -c Read free energy + 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 + ishift1=ishift1+1 + ibeg=2 +! 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 +c iii=0 + endif +! Read free energy if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp -C Fish out the ATOM cards. +! 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 +c write (2,'(a)') card +! 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 +! write (iout,*) "ires",ires,ires-ishift+ishift1, +! & " ires_old",ires_old +! write (iout,*) "ishift",ishift," ishift1",ishift1 +! 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) +! 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 +! write (iout,*) "Calculating sidechain center iii",iii if (unres_pdb) then do j=1,3 - dc(j,ires)=sccor(j,iii) + dc(j,ires+nres)=sccor(j,iii) enddo else call sccenter(ires_old,iii,sccor) endif iii=0 endif -C Start new residue. +! Start new residue. if (res.eq.'Cl-' .or. res.eq.'Na+') then ires=ires_old cycle @@ -93,9 +114,17 @@ c write (iout,*) "BEG ires",ires endif ires=ires-ishift+ishift1 ires_old=ires -c write (iout,*) "ishift",ishift," ires",ires, -c & " ires_old",ires_old - ibeg=0 +! 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 !!!!! + ishift1=ishift1-1 !!!!! +! 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 @@ -109,15 +138,15 @@ c & " ires_old",ires_old else ires=ires-ishift+ishift1 endif -c write (iout,*) "ires_old",ires_old," ires",ires +! 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 +! ishift1=ishift1+1 endif -c write (2,*) "ires",ires," res ",res," ity",ity +! 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 +! write (iout,*) "backbone ",atom #ifdef DEBUG write (iout,'(2i3,2x,a,3f8.3)') & ires,itype(ires),res,(c(j,ires),j=1,3) @@ -126,19 +155,15 @@ c write (iout,*) "backbone ",atom 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. +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 -c write (iout,*) "sidechain ",atom +! 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 @@ -474,22 +499,36 @@ c--------------------------------------------------------------------------- end c--------------------------------------------------------------------------- subroutine bond_regular - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' + implicit none + include 'DIMENSIONS' include 'COMMON.VAR' - include 'COMMON.LOCAL' - include 'COMMON.CALC' + 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)=1.0d0/vbld(i+1) - vbld(i+1+nres)=dsc(itype(i+1)) - vbld_inv(i+1+nres)=dsc_inv(itype(i+1)) + 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 +c--------------------------------------------------------------------------- subroutine readpdb_template(k) C Read the PDB file with gaps for read_constr_homology with read2sigma C and convert the peptide geometry into virtual-chain geometry.