X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-HCD%2Freadpdb.F;h=83c63abcede45c2f7544f0ee1ddf1dcda2712735;hb=df61eb1a0ad598d7c6c5b4037dee4bec200d5bc2;hp=b8ce4f4c843b0d19aedfd9674772dab561bdc79c;hpb=1346fb3959c2eb0a370b11bc6ccad5e4cca27ec9;p=unres.git diff --git a/source/wham/src-HCD/readpdb.F b/source/wham/src-HCD/readpdb.F index b8ce4f4..83c63ab 100644 --- a/source/wham/src-HCD/readpdb.F +++ b/source/wham/src-HCD/readpdb.F @@ -13,78 +13,156 @@ C geometry. include 'COMMON.GEO' include 'COMMON.NAMES' include 'COMMON.SBRIDGE' + include 'COMMON.FRAG' character*3 seq,atom,res character*80 card 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 + integer iterter(maxres) + double precision efree_temp + iii=0 ibeg=1 ishift1=0 + sccalc=.false. + ires=0 do read (ipdbin,'(a80)',end=10) card +c 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) + 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 -C End current chain -c ires_old=ires+1 +! 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 + ishift1=ishift1+1 ibeg=2 -c write (iout,*) "Chain ended",ires,ishift,ires_old - call sccenter(ires,iii,sccor) + 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 + iii=0 + sccalc=.true. endif -C Fish out the ATOM cards. +! Read free energy + if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp +! 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 -C Calculate the CM of the preceding residue. + sccalc=.false. + read (card(12:16),*) atom +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 +! 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 +! Calculate the CM of the preceding residue. +! if (ibeg.eq.0) call sccenter(ires,iii,sccor) if (ibeg.eq.0) then - call sccenter(ires,iii,sccor) +! 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_old,iii,sccor) + endif + iii=0 + sccalc=.true. endif -C Start new residue. -c write (iout,'(a80)') card - read (card(23:26),*) ires - read (card(18:20),'(a3)') res - if (ibeg.eq.1) then +! 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 -c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift - ibeg=0 + 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 -c Start a new chain - ishift=-ires_old+ires-1 -c write (iout,*) "New chain started",ires,ishift +! 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 + 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 +! 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 +! 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) - read(card(61:66),*) bfac(ires) -c write (iout,'(2i3,2x,a,3f8.3,5x,f8.3)') -c & ires,itype(ires),res,(c(j,ires),j=1,3),bfac(ires) - iii=1 +! 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(1:1).ne.'Q' .and. atom(1:2).ne.'1H' .and. - & atom(1:2).ne.'2H' .and. atom(1:2).ne.'3H' .and. - & atom.ne.'N ' .and. atom.ne.'C ' .and. - & atom.ne.'OXT' ) then +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 -c write (iout,*) res,ires,iii,atom read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3) -c write (iout,'(3f8.3)') (sccor(j,iii),j=1,3) +c write (2,*) "iii",iii endif endif enddo @@ -141,7 +219,7 @@ C endif !unres_pdb endif !itype.eq.ntyp1 enddo C Calculate the CM of the last side chain. - call sccenter(ires,iii,sccor) + if (.not. sccalc) call sccenter(ires,iii,sccor) nsup=nres nstart_sup=1 if (itype(nres).ne.10) then @@ -410,20 +488,33 @@ 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_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---------------------------------------------------------------------------