X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fio.f90;h=a86fc0b97d5808a630ef6c02a241bdd1bdfd3592;hb=340832b9074a6903554ccfcf3cac2abf65e09d3a;hp=379978e31142cd3ddc053513c50d58113d00eb46;hpb=8d2ab9ba185dbbc31bfe3d1c66d7e1c9d632463b;p=unres4.git diff --git a/source/unres/io.f90 b/source/unres/io.f90 index 379978e..a86fc0b 100644 --- a/source/unres/io.f90 +++ b/source/unres/io.f90 @@ -220,12 +220,12 @@ DO WHILE (FAIL .AND. ICOUNT_FAIL .LE. MAXCOUNT_FAIL) do i=nnt,nct - if (itype(i).ne.10) then -!d print *,'i=',i,' itype=',itype(i),' theta=',theta(i+1) + if (itype(i,1).ne.10) then +!d print *,'i=',i,' itype=',itype(i,1),' theta=',theta(i+1) fail=.true. ii=0 do while (fail .and. ii .le. maxsi) - call gen_side(itype(i),theta(i+1),alph(i),omeg(i),fail) + call gen_side(itype(i,1),theta(i+1),alph(i),omeg(i),fail) ii = ii+1 enddo endif @@ -716,11 +716,11 @@ ! include 'COMMON.BOUNDS' ! include 'COMMON.MD' ! include 'COMMON.SETUP' - character(len=4),dimension(:),allocatable :: sequence !(maxres) + character(len=4),dimension(:,:),allocatable :: sequence !(maxres,maxmolecules) ! integer :: rescode ! double precision x(maxvar) character(len=256) :: pdbfile - character(len=320) :: weightcard + character(len=800) :: weightcard character(len=80) :: weightcard_t!,ucase ! integer,dimension(:),allocatable :: itype_pdb !(maxres) ! common /pizda/ itype_pdb @@ -741,13 +741,14 @@ !----------------------------- allocate(c(3,2*maxres+2)) !(3,maxres2+2) maxres2=2*maxres allocate(dc(3,0:2*maxres)) !(3,0:maxres2) - allocate(itype(maxres)) !(maxres) + allocate(itype(maxres,5)) !(maxres) + allocate(istype(maxres)) ! ! Zero out tables. ! c(:,:)=0.0D0 dc(:,:)=0.0D0 - itype(:)=0 + itype(:,:)=0 !----------------------------- ! ! Body @@ -768,6 +769,19 @@ call reada(weightcard,'WTURN6',wturn6,1.0D0) call reada(weightcard,'WSCCOR',wsccor,1.0D0) call reada(weightcard,'WSTRAIN',wstrain,1.0D0) + call reada(weightcard,'WVDWPP_NUCL',wvdwpp_nucl,1.0D0) + call reada(weightcard,'WELPP',welpp,1.0d0) + call reada(weightcard,'WVDWPSB',wvdwpsb,1.0d0) + call reada(weightcard,'WELPSB',welpsb,1.0D0) + call reada(weightcard,'WVDWSB',wvdwsb,1.0d0) + call reada(weightcard,'WELSB',welsb,1.0D0) + call reada(weightcard,'WBOND_NUCL',wbond_nucl,1.0D0) + call reada(weightcard,'WANG_NUCL',wang_nucl,1.0D0) + call reada(weightcard,'WSBLOC',wsbloc,1.0D0) + call reada(weightcard,'WTOR_NUCL',wtor_nucl,1.0D0) + call reada(weightcard,'WTORD_NUCL',wtor_d_nucl,1.0D0) + call reada(weightcard,'WCORR_NUCL',wcorr_nucl,1.0D0) + call reada(weightcard,'WCORR3_NUCL',wcorr3_nucl,1.0D0) call reada(weightcard,'WBOND',wbond,1.0D0) call reada(weightcard,'WTOR',wtor,1.0D0) call reada(weightcard,'WTORD',wtor_d,1.0D0) @@ -783,6 +797,7 @@ call reada(weightcard,'DELT_CORR',delt_corr,0.5d0) call reada(weightcard,'TEMP0',temp0,300.0d0) if (index(weightcard,'SOFT').gt.0) ipot=6 + call reada(weightcard,'WBOND_NUCL',wbond_nucl,1.0D0) ! 12/1/95 Added weight for the multi-body term WCORR call reada(weightcard,'WCORRH',wcorr,1.0D0) if (wcorr4.gt.0.0d0) wcorr=wcorr4 @@ -935,7 +950,7 @@ !el if(.not.allocated(itype_pdb)) allocate(itype_pdb(nres)) do i=1,nres - itype_pdb(i)=itype(i) + itype_pdb(i)=itype(i,1) enddo close (ipdbin) nnt=nstart_sup @@ -949,8 +964,8 @@ write(iout,*)'Adding sidechains' maxsi=1000 do i=2,nres-1 - iti=itype(i) - if (iti.ne.10 .and. itype(i).ne.ntyp1) then + iti=itype(i,1) + if (iti.ne.10 .and. itype(i,1).ne.ntyp1) then nsi=0 fail=.true. do while (fail.and.nsi.le.maxsi) @@ -963,21 +978,61 @@ enddo endif endif - + if (indpdb.eq.0) then + nres_molec(:)=0 + allocate(sequence(maxres,5)) + + if (protein) then ! Read sequence if not taken from the pdb file. - read (inp,*) nres + molec=1 + read (inp,*) nres_molec(molec) ! print *,'nres=',nres - allocate(sequence(nres)) if (iscode.gt.0) then - read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres) + read (inp,'(80a1)') (sequence(i,molec)(1:1),i=1,nres_molec(molec)) else - read (inp,'(20(1x,a3))') (sequence(i),i=1,nres) + read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec)) endif ! Convert sequence to numeric code - do i=1,nres - itype(i)=rescode(i,sequence(i),iscode) + + do i=1,nres_molec(molec) + itype(i,1)=rescode(i,sequence(i,molec),iscode,molec) + enddo + endif + if (nucleic) then +! Read sequence if not taken from the pdb file. + molec=2 + read (inp,*) nres_molec(molec) +! print *,'nres=',nres +! allocate(sequence(maxres,5)) +! if (iscode.gt.0) then + read (inp,'(20a4)') (sequence(i,molec),i=1,nres_molec(molec)) +! Convert sequence to numeric code + + do i=1,nres_molec(molec) + istype(i)=sugarcode(sequence(i,molec)(1:1),i) + itype(i,1)=rescode(i,sequence(i,molec)(2:2),iscode,molec) enddo + endif + + if (ions) then +! Read sequence if not taken from the pdb file. + molec=5 + read (inp,*) nres_molec(molec) +! print *,'nres=',nres + read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec)) +! Convert sequence to numeric code + print *,nres_molec(molec) + do i=1,nres_molec(molec) + itype(i,1)=rescode(i,sequence(i,molec),iscode,molec) + enddo + endif + nres=0 + do i=1,5 + nres=nres+nres_molec(i) + print *,nres_molec(i) + enddo + ! Assign initial virtual bond lengths !elwrite(iout,*) "test_alloc" if(.not.allocated(vbld)) allocate(vbld(2*nres)) @@ -989,14 +1044,14 @@ vbld_inv(i)=vblinv enddo do i=2,nres-1 - vbld(i+nres)=dsc(iabs(itype(i))) - vbld_inv(i+nres)=dsc_inv(iabs(itype(i))) -! write (iout,*) "i",i," itype",itype(i), -! & " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres) + vbld(i+nres)=dsc(iabs(itype(i,1))) + vbld_inv(i+nres)=dsc_inv(iabs(itype(i,1))) +! write (iout,*) "i",i," itype",itype(i,1), +! & " dsc",dsc(itype(i,1))," vbld",vbld(i),vbld(i+nres) enddo endif ! print *,nres -! print '(20i4)',(itype(i),i=1,nres) +! print '(20i4)',(itype(i,1),i=1,nres) !---------------------------- !el reallocate tables ! do i=1,maxres2 @@ -1006,8 +1061,8 @@ ! enddo ! enddo ! do i=1,maxres -!elwrite(iout,*) "itype",i,itype(i) -! itype_alloc(i)=itype(i) +!elwrite(iout,*) "itype",i,itype(i,1) +! itype_alloc(i)=itype(i,1) ! enddo ! deallocate(c) @@ -1026,21 +1081,21 @@ ! enddo ! enddo ! do i=1,nres+2 -! itype(i)=itype_alloc(i) +! itype(i,1)=itype_alloc(i) ! itel(i)=0 ! enddo !-------------------------- do i=1,nres #ifdef PROCOR - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) then #else - if (itype(i).eq.ntyp1) then + if (itype(i,1).eq.ntyp1) then #endif itel(i)=0 #ifdef PROCOR - else if (iabs(itype(i+1)).ne.20) then + else if (iabs(itype(i+1,1)).ne.20) then #else - else if (iabs(itype(i)).ne.20) then + else if (iabs(itype(i,1)).ne.20) then #endif itel(i)=1 else @@ -1050,7 +1105,7 @@ if(me.eq.king.or..not.out1file)then write (iout,*) "ITEL" do i=1,nres-1 - write (iout,*) i,itype(i),itel(i) + write (iout,*) i,itype(i,1),itel(i) enddo print *,'Call Read_Bridge.' endif @@ -1139,22 +1194,22 @@ write (iout,'(a)') 'Boundaries in phi angle sampling:' do i=1,nres write (iout,'(a3,i5,2f10.1)') & - restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg + restyp(itype(i,1),1),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg enddo #ifdef MP endif #endif nct=nres -!d print *,'NNT=',NNT,' NCT=',NCT - if (itype(1).eq.ntyp1) nnt=2 - if (itype(nres).eq.ntyp1) nct=nct-1 + print *,'NNT=',NNT,' NCT=',NCT + if (itype(1,molnum(1)).eq.ntyp1_molec(molnum(1))) nnt=2 + if (itype(nres,molnum(nres)).eq.ntyp1_molec(molnum(nres))) nct=nct-1 if (pdbref) then if(me.eq.king.or..not.out1file) & write (iout,'(a,i3)') 'nsup=',nsup nstart_seq=nnt if (nsup.le.(nct-nnt+1)) then do i=0,nct-nnt+1-nsup - if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then + if (seq_comp(itype(nnt+i,1),itype_pdb(nstart_sup),nsup)) then nstart_seq=nnt+i goto 111 endif @@ -1164,7 +1219,7 @@ stop else do i=0,nsup-(nct-nnt+1) - if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1)) & + if (seq_comp(itype(nnt,1),itype_pdb(nstart_sup+i),nct-nnt+1)) & then nstart_sup=nstart_sup+i nsup=nct-nnt+1 @@ -1234,9 +1289,9 @@ icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup enddo if(me.eq.king.or..not.out1file) & - write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',& + write (2,*) i,' ',restyp(itype(icont_ref(1,i),1),1),' ',& icont_ref(1,i),' ',& - restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i) + restyp(itype(icont_ref(2,i),1),1),' ',icont_ref(2,i) enddo endif endif @@ -1265,7 +1320,7 @@ enddo enddo do i=nnt,nct - if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then + if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then do j=1,3 dc(j,i+nres)=c(j,i+nres)-c(j,i) dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres) @@ -1298,7 +1353,7 @@ !elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres) do i=2,nres-1 omeg(i)=-120d0*deg2rad - if (itype(i).le.0) omeg(i)=-omeg(i) + if (itype(i,1).le.0) omeg(i)=-omeg(i) enddo else if(me.eq.king.or..not.out1file) & @@ -1388,11 +1443,11 @@ do i=1,nss i1=ihpb(i)-nres i2=jhpb(i)-nres - it1=itype(i1) - it2=itype(i2) + it1=itype(i1,1) + it2=itype(i2,1) if (me.eq.king.or..not.out1file) & write (iout,'(2a,i3,3a,i3,a,3f10.3)') & - restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),& + restyp(it1,1),'(',i1,') -- ',restyp(it2,1),'(',i2,')',dhpb(i),& ebr,forcon(i) enddo write (iout,'(a)')