include 'COMMON.CONTROL'
include 'COMMON.SBRIDGE'
include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
logical file_exist
C Read force-field parameters except weights
call parmread
C Set up the time limit (caution! The time must be input in minutes!)
read_cart=index(controlcard,'READ_CART').gt.0
call readi(controlcard,'CONSTR_DIST',constr_dist,0)
+ call readi(controlcard,'CONSTR_HOMOL',constr_homology,0)
+ read_homol_frag = index(controlcard,"READ_HOMOL_FRAG").gt.0
call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
sideadd=(index(controlcard,'SIDEADD').gt.0)
energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
outpdb=(index(controlcard,'PDBOUT').gt.0)
+ outx=(index(controlcard,'XOUT').gt.0)
outmol2=(index(controlcard,'MOL2OUT').gt.0)
pdbref=(index(controlcard,'PDBREF').gt.0)
refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
modecalc=1
refstr=.true.
endif
+ call reada(controlcard,"CHECKGRAD_INC",checkgrad_inc,1.0d-4)
if (index(controlcard,'CHECKGRAD').gt.0) then
modecalc=5
if (index(controlcard,'CART').gt.0) then
endif
call reada(controlcard,"Q_NP",Q_np,0.1d0)
usampl = index(controlcard,"USAMPL").gt.0
-
mdpdb = index(controlcard,"MDPDB").gt.0
call reada(controlcard,"T_BATH",t_bath,300.0d0)
call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
large = index(controlcard,"LARGE").gt.0
print_compon = index(controlcard,"PRINT_COMPON").gt.0
rattle = index(controlcard,"RATTLE").gt.0
+ preminim = index(controlcard,"PREMINIM").gt.0
+ if (preminim) then
+ dccart=(index(controlcard,'CART').gt.0)
+ call read_minim
+ endif
c if performing umbrella sampling, fragments constrained are read from the fragment file
nset=0
if(usampl) then
write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
if (rattle) write (iout,'(a60)')
& "Rattle algorithm used to constrain the virtual bonds"
+ if (preminim .or. iranconf.gt.0) then
+ write (iout,'(a60)')
+ & "Initial structure will be energy-minimized"
+ endif
endif
reset_fricmat=1000
if (lang.gt.0) then
common /pizda/ itype_pdb
logical seq_comp,fail
double precision energia(0:n_ene)
+
integer ilen
external ilen
C
call reada(weightcard,'WTORD',wtor_d,1.0D0)
call reada(weightcard,'WANG',wang,1.0D0)
call reada(weightcard,'WSCLOC',wscloc,1.0D0)
+ call reada(weightcard,'WDFAD',wdfa_dist,0.0d0)
+ call reada(weightcard,'WDFAT',wdfa_tor,0.0d0)
+ call reada(weightcard,'WDFAN',wdfa_nei,0.0d0)
+ call reada(weightcard,'WDFAB',wdfa_beta,0.0d0)
call reada(weightcard,'SCAL14',scal14,0.4D0)
call reada(weightcard,'SCALSCP',scalscp,1.0d0)
call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
weights(18)=scal14
weights(21)=wsccor
endif
+ weights(25)=wdfa_dist
+ weights(26)=wdfa_tor
+ weights(27)=wdfa_nei
+ weights(28)=wdfa_beta
if(me.eq.king.or..not.out1file)
& write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
& wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
- & wturn4,wturn6
+ & wturn4,wturn6,
+ & wdfa_dist,wdfa_tor,wdfa_nei,wdfa_beta
10 format (/'Energy-term weights (unscaled):'//
& 'WSCC= ',f10.6,' (SC-SC)'/
& 'WSCP= ',f10.6,' (SC-p)'/
& 'WSCCOR= ',f10.6,' (back-scloc correlation)'/
& 'WTURN3= ',f10.6,' (turns, 3rd order)'/
& 'WTURN4= ',f10.6,' (turns, 4th order)'/
- & 'WTURN6= ',f10.6,' (turns, 6th order)')
+ & 'WTURN6= ',f10.6,' (turns, 6th order)'/
+ & 'WDFA_D= ',f10.6,' (DFA, distance)' /
+ & 'WDFA_T= ',f10.6,' (DFA, torsional)' /
+ & 'WDFA_N= ',f10.6,' (DFA, number of neighbor)' /
+ & 'WDFA_B= ',f10.6,' (DFA, beta formation)')
if(me.eq.king.or..not.out1file)then
if (wcorr4.gt.0.0d0) then
write (iout,'(/2a/)') 'Local-electrostatic type correlation ',
if(me.eq.king.or..not.out1file)
& write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
& wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
- & wturn4,wturn6
+ & wturn4,wturn6,
+ & wdfa_dist,wdfa_tor,wdfa_nei,wdfa_beta
22 format (/'Energy-term weights (scaled):'//
& 'WSCC= ',f10.6,' (SC-SC)'/
& 'WSCP= ',f10.6,' (SC-p)'/
& 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/
& 'WTURN3= ',f10.6,' (turns, 3rd order)'/
& 'WTURN4= ',f10.6,' (turns, 4th order)'/
- & 'WTURN6= ',f10.6,' (turns, 6th order)')
+ & 'WTURN6= ',f10.6,' (turns, 6th order)'/
+ & 'WDFA_D= ',f10.6,' (DFA, distance)' /
+ & 'WDFA_T= ',f10.6,' (DFA, torsional)' /
+ & 'WDFA_N= ',f10.6,' (DFA, number of neighbor)' /
+ & 'WDFA_B= ',f10.6,' (DFA, beta formation)')
if(me.eq.king.or..not.out1file)
& write (iout,*) "Reference temperature for weights calculation:",
& temp0
34 continue
c print *,'Begin reading pdb data'
call readpdb
+ do i=1,2*nres
+ do j=1,3
+ crefjlee(j,i)=c(j,i)
+ enddo
+ enddo
+#ifdef DEBUG
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
+ & (crefjlee(j,i+nres),j=1,3)
+ enddo
+#endif
c print *,'Finished reading pdb data'
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3,a,i3)')'nsup=',nsup,
call chainbuild
endif
C Following 2 lines for diagnostics; comment out if not needed
- write (iout,*) "After sideadd"
- call intout
+c write (iout,*) "After sideadd"
+c call intout
endif
if (indpdb.eq.0) then
C Read sequence if not taken from the pdb file.
do i=1,nres
itype(i)=rescode(i,sequence(i),iscode)
enddo
+ if (itype(2).eq.10.and.itype(1).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the first full residue, initial dummy deleted"
+ do i=1,nres
+ itype(i)=itype(i+1)
+ enddo
+ nres=nres-1
+ endif
+ if (itype(nres-1).eq.10.and.itype(nres).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the last full residue, terminal dummy deleted"
+ nres=nres-1
+ endif
+
C Assign initial virtual bond lengths
do i=2,nres
vbld(i)=vbl
cd print *,'NNT=',NNT,' NCT=',NCT
if (itype(1).eq.21) nnt=2
if (itype(nres).eq.21) nct=nct-1
+
+C Bartek:READ init_vars
+C Initialize variables!
+C Juyong:READ read_info
+C READ fragment information!!
+C both routines should be in dfa.F file!!
+
+#ifdef DFA
+ if (.not. (wdfa_dist.eq.0.0 .and. wdfa_tor.eq.0.0 .and.
+ & wdfa_nei.eq.0.0 .and. wdfa_beta.eq.0.0)) then
+ call init_dfa_vars
+ print*, 'init_dfa_vars finished!'
+ call read_dfa_info
+ print*, 'read_dfa_info finished!'
+ endif
+#endif
+C
if (pdbref) then
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3)') 'nsup=',nsup
c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
if (constr_dist.gt.0) then
call read_dist_constr
- call hpb_partition
endif
+
+
+ if (constr_homology.gt.0) then
+ call read_constr_homology
+ if (indpdb.gt.0 .or. pdbref) then
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=crefjlee(j,i)
+ cref(j,i)=crefjlee(j,i)
+ enddo
+ enddo
+ endif
+#ifdef DEBUG
+ write (iout,*) "Array C"
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(c(j,i),j=1,3),
+ & (c(j,i+nres),j=1,3)
+ enddo
+ write (iout,*) "Array Cref"
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(cref(j,i),j=1,3),
+ & (cref(j,i+nres),j=1,3)
+ enddo
+#endif
+ call int_from_cart1(.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ enddo
+ do i=1,nres-1
+ do j=1,3
+ dc(j,i)=c(j,i+1)-c(j,i)
+ dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
+ enddo
+ enddo
+ do i=2,nres-1
+ do j=1,3
+ dc(j,i+nres)=c(j,i+nres)-c(j,i)
+ dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
+ enddo
+ enddo
+ else
+ homol_nset=0
+ endif
+
+
+ if (nhpb.gt.0) call hpb_partition
c write (iout,*) "After read_dist_constr nhpb",nhpb
c call flush(iout)
if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
if(me.eq.king.or..not.out1file .and.fg_rank.eq.0)
& write (iout,'(a)') 'Initial geometry will be read in.'
if (read_cart) then
+ read (inp,*) time,potE,uconst,t_bath,
+ & nss,(ihpb(j),jhpb(j),j=1,nss), nn, (qfrag(i),i=1,nn)
read(inp,'(8f10.5)',end=36,err=36)
& ((c(l,k),l=1,3),k=1,nres),
& ((c(l,k+nres),l=1,3),k=nnt,nct)
enddo
endif
enddo
- return
+c return
else
call read_angles(inp,*36)
endif
if (nthread.gt.0) then
call read_threadbase
endif
+ write (iout,*) "READRTNS: Calling setup_var"
+ call flush(iout)
call setup_var
if (me.eq.king .or. .not. out1file)
& call intout
write (iout,'(20i4)') (iss(i),i=1,ns)
if (dyn_ss) then
write(iout,*)"Running with dynamic disulfide-bond formation"
- do i=nss+1,nhpb
- ihpb(i-nss)=ihpb(i)
- jhpb(i-nss)=jhpb(i)
- forcon(i-nss)=forcon(i)
- dhpb(i-nss)=dhpb(i)
- enddo
- nhpb=nhpb-nss
- nss=0
- call hpb_partition
- do i=1,ns
- dyn_ss_mask(iss(i))=.true.
- enddo
else
write (iout,'(/a/)') 'Pre-formed links are:'
do i=1,nss
i2=jhpb(i)-nres
it1=itype(i1)
it2=itype(i2)
- if (me.eq.king.or..not.out1file)
- & write (iout,'(2a,i3,3a,i3,a,3f10.3)')
+ write (iout,'(2a,i3,3a,i3,a,3f10.3)')
& restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
& ebr,forcon(i)
enddo
write (iout,'(a)')
endif
endif
+ if (ns.gt.0.and.dyn_ss) then
+ do i=nss+1,nhpb
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+ enddo
+ endif
if (i2ndstr.gt.0) call secstrp2dihc
c call geom_to_var(nvar,x)
c call etotal(energia(0))
do i=1,ns
if (itype(iss(i)).ne.1) then
if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)')
- & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
+ & 'Do you REALLY think that the residue ',
+ & restyp(itype(iss(i))),i,
& ' can form a disulfide bridge?!!!'
write (*,'(2a,i3,a)')
- & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
+ & 'Do you REALLY think that the residue ',
+ & restyp(itype(iss(i))),i,
& ' can form a disulfide bridge?!!!'
#ifdef MPI
call MPI_Finalize(MPI_COMM_WORLD,ierror)
C Read preformed bridges.
if (ns.gt.0) then
read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
- write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
+ if(fg_rank.eq.0)
+ & write(iout,*)'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
if (nss.gt.0) then
nhpb=nss
C Check if the residues involved in bridges are in the specified list of
& //'.pdb'
mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//
& liczba(:ilen(liczba))//'.mol2'
+ cartname=prefix(:lenpre)//'_'//pot(:lenpot)//
+ & liczba(:ilen(liczba))//'.x'
statname=prefix(:lenpre)//'_'//pot(:lenpot)//
& liczba(:ilen(liczba))//'.stat'
if (lentmp.gt.0)
intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
+ cartname=prefix(:lenpre)//'_'//pot(:lenpot)//'.x'
statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
if (lentmp.gt.0)
& call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
include 'COMMON.CHAIN'
include 'COMMON.IOUNITS'
include 'COMMON.MD'
+ include 'COMMON.CONTROL'
open(irest2,file=rest2name,status='unknown')
read(irest2,*) totT,EK,potE,totE,t_bath
do i=1,2*nres
do i=1,2*nres
read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
enddo
- if(usampl) then
+ if(usampl.or.homol_nset.gt.1) then
read (irest2,*) iset
endif
close(irest2)
include 'COMMON.IOUNITS'
include 'COMMON.MD'
include 'COMMON.CONTROL'
+ integer iset1
read(inp,*) nset,nfrag,npair,nfrag_back
if(me.eq.king.or..not.out1file)
& write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,
& " nfrag_back",nfrag_back
- do iset=1,nset
- read(inp,*) mset(iset)
+ do iset1=1,nset
+ read(inp,*) mset(iset1)
do i=1,nfrag
- read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),
- & qinfrag(i,iset)
+ read(inp,*) wfrag(i,iset1),ifrag(1,i,iset1),ifrag(2,i,iset1),
+ & qinfrag(i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),
- & ifrag(2,i,iset), qinfrag(i,iset)
+ & write(iout,*) "R ",i,wfrag(i,iset1),ifrag(1,i,iset1),
+ & ifrag(2,i,iset1), qinfrag(i,iset1)
enddo
do i=1,npair
- read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),
- & qinpair(i,iset)
+ read(inp,*) wpair(i,iset1),ipair(1,i,iset1),ipair(2,i,iset1),
+ & qinpair(i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),
- & ipair(2,i,iset), qinpair(i,iset)
+ & write(iout,*) "R ",i,wpair(i,iset1),ipair(1,i,iset1),
+ & ipair(2,i,iset1), qinpair(i,iset1)
enddo
do i=1,nfrag_back
- read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),
- & wfrag_back(3,i,iset),
- & ifrag_back(1,i,iset),ifrag_back(2,i,iset)
+ read(inp,*) wfrag_back(1,i,iset1),wfrag_back(2,i,iset1),
+ & wfrag_back(3,i,iset1),
+ & ifrag_back(1,i,iset1),ifrag_back(2,i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),
- & wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
+ & write(iout,*) "A",i,wfrag_back(1,i,iset1),
+ & wfrag_back(2,i,iset1),
+ & wfrag_back(3,i,iset1),ifrag_back(1,i,iset1),
+ & ifrag_back(2,i,iset1)
enddo
enddo
return
call readi(controlcard,"NPAIR",npair_,0)
call readi(controlcard,"NDIST",ndist_,0)
call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
+
call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
if (wfrag_(i).gt.0.0d0) then
do j=ifrag_(1,i),ifrag_(2,i)-1
do k=j+1,ifrag_(2,i)
- write (iout,*) "j",j," k",k
+c write (iout,*) "j",j," k",k
ddjk=dist(j,k)
if (constr_dist.eq.1) then
nhpb=nhpb+1
endif
enddo
do i=1,ndist_
+ if (constr_dist.eq.11) then
+ read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
+ & ibecarb(i),forcon(nhpb+1),fordepth(nhpb+1)
+ fordepth(nhpb+1)=fordepth(nhpb+1)/forcon(nhpb+1)
+ else
read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
& ibecarb(i),forcon(nhpb+1)
+ endif
if (forcon(nhpb+1).gt.0.0d0) then
nhpb=nhpb+1
if (ibecarb(i).gt.0) then
if (.not.out1file .or. me.eq.king) then
#endif
do i=1,nhpb
+ if (constr_dist.eq.11) then
+ write (iout,'(a,3i5,2f8.2,i2,2f10.1)') "+dist.constr11 ",
+ & i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i),
+ & fordepth(i)
+ else
write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ",
& i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i)
+ endif
enddo
call flush(iout)
#ifdef MPI
return
end
c-------------------------------------------------------------------------------
+
+ subroutine read_constr_homology
+
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.MD'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+c
+c For new homol impl
+c
+ include 'COMMON.VAR'
+c
+
+c double precision odl_temp,sigma_odl_temp,waga_theta,waga_d,
+c & dist_cut
+c common /przechowalnia/ odl_temp(maxres,maxres,max_template),
+c & sigma_odl_temp(maxres,maxres,max_template)
+ character*2 kic2
+ character*24 model_ki_dist, model_ki_angle
+ character*500 controlcard
+ integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
+ logical lprn /.true./
+ integer ilen
+ external ilen
+ logical liiflag
+c
+c FP - Nov. 2014 Temporary specifications for new vars
+c
+ double precision rescore_tmp,x12,y12,z12,rescore2_tmp
+ double precision, dimension (max_template,maxres) :: rescore
+ double precision, dimension (max_template,maxres) :: rescore2
+ character*24 pdbfile,tpl_k_rescore
+c -----------------------------------------------------------------
+c Reading multiple PDB ref structures and calculation of retraints
+c not using pre-computed ones stored in files model_ki_{dist,angle}
+c FP (Nov., 2014)
+c -----------------------------------------------------------------
+c
+c
+c Alternative: reading from input
+ call card_concat(controlcard)
+ call reada(controlcard,"HOMOL_DIST",waga_dist,1.0d0)
+ call reada(controlcard,"HOMOL_ANGLE",waga_angle,1.0d0)
+ call reada(controlcard,"HOMOL_THETA",waga_theta,1.0d0) ! new
+ call reada(controlcard,"HOMOL_SCD",waga_d,1.0d0) ! new
+ call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
+ call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
+ call readi(controlcard,"HOMOL_NSET",homol_nset,1)
+ read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
+ start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0)
+ if(.not.read2sigma.and.start_from_model) then
+ write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA'
+ start_from_model=.false.
+ endif
+ if(start_from_model) write(iout,*) 'START_FROM_MODELS is ON'
+ if(start_from_model .and. rest) then
+ write(iout,*) 'START_FROM_MODELS is OFF'
+ write(iout,*) 'remove restart keyword from input'
+ endif
+ if (homol_nset.gt.1)then
+ call card_concat(controlcard)
+ read(controlcard,*) (waga_homology(i),i=1,homol_nset)
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "iset homology_weight "
+ do i=1,homol_nset
+ write(iout,*) i,waga_homology(i)
+ enddo
+ endif
+ iset=mod(kolor,homol_nset)+1
+ else
+ iset=1
+ waga_homology(1)=1.0
+ endif
+
+cd write (iout,*) "nnt",nnt," nct",nct
+cd call flush(iout)
+
+
+ lim_odl=0
+ lim_dih=0
+c
+ write(iout,*) 'nnt=',nnt,'nct=',nct
+c
+ do i = nnt,nct
+ do k=1,constr_homology
+ idomain(k,i)=0
+ enddo
+ enddo
+
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ ii_in_use(ii)=0
+ enddo
+ enddo
+
+ if (read_homol_frag) then
+ call read_klapaucjusz
+ else
+
+ do k=1,constr_homology
+
+ read(inp,'(a)') pdbfile
+c Next stament causes error upon compilation (?)
+c if(me.eq.king.or. .not. out1file)
+c write (iout,'(2a)') 'PDB data will be read from file ',
+c & pdbfile(:ilen(pdbfile))
+ write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ open(ipdbin,file=pdbfile,status='old',err=33)
+ goto 34
+ 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ stop
+ 34 continue
+c print *,'Begin reading pdb data'
+c
+c Files containing res sim or local scores (former containing sigmas)
+c
+
+ write(kic2,'(bz,i2.2)') k
+
+ tpl_k_rescore="template"//kic2//".sco"
+
+ unres_pdb=.false.
+ if (read2sigma) then
+ call readpdb_template(k)
+ else
+ call readpdb
+ endif
+c
+c Distance restraints
+c
+c ... --> odl(k,ii)
+C Copy the coordinates from reference coordinates (?)
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=cref(j,i)
+c write (iout,*) "c(",j,i,") =",c(j,i)
+ enddo
+ enddo
+c
+c From read_dist_constr (commented out 25/11/2014 <-> res sim)
+c
+c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
+ open (ientin,file=tpl_k_rescore,status='old')
+ if (nnt.gt.1) rescore(k,1)=0.0d0
+ do irec=nnt,nct ! loop for reading res sim
+ if (read2sigma) then
+ read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
+ & idomain_tmp
+ i_tmp=i_tmp+nnt-1
+ idomain(k,i_tmp)=idomain_tmp
+ rescore(k,i_tmp)=rescore_tmp
+ rescore2(k,i_tmp)=rescore2_tmp
+ write(iout,'(a7,i5,2f10.5,i5)') "rescore",
+ & i_tmp,rescore2_tmp,rescore_tmp,
+ & idomain_tmp
+ else
+ idomain(k,irec)=1
+ read (ientin,*,end=1401) rescore_tmp
+
+c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
+ rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
+c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
+ endif
+ enddo
+ 1401 continue
+ close (ientin)
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+
+ x12=c(1,i)-c(1,j)
+ y12=c(2,i)-c(2,j)
+ z12=c(3,i)-c(3,j)
+ distal=dsqrt(x12*x12+y12*y12+z12*z12)
+c write (iout,*) k,i,j,distal,dist2_cut
+
+ if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+ & .and. distal.le.dist2_cut ) then
+
+ ii=ii+1
+ ii_in_use(ii)=1
+ l_homo(k,ii)=.true.
+
+c write (iout,*) "k",k
+c write (iout,*) "i",i," j",j," constr_homology",
+c & constr_homology
+ ires_homo(ii)=i
+ jres_homo(ii)=j
+ odl(k,ii)=distal
+ if (read2sigma) then
+ sigma_odl(k,ii)=0
+ do ik=i,j
+ sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
+ enddo
+ sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
+ if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
+ & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+ else
+ if (odl(k,ii).le.dist_cut) then
+ sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
+ else
+#ifdef OLDSIGMA
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
+#else
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+#endif
+ endif
+ endif
+ sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
+ else
+ ii=ii+1
+ l_homo(k,ii)=.false.
+ endif
+ enddo
+ enddo
+ lim_odl=ii
+ endif
+c
+c Theta, dihedral and SC retraints
+c
+ if (waga_angle.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_dih,status='old')
+c do irec=1,maxres-3 ! loop for reading sigma_dih
+c read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
+c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
+c sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_dih(k,i+nnt-1)
+c enddo
+c1402 continue
+c close (ientin)
+ do i = nnt+3,nct
+ if (idomain(k,i).eq.0) then
+ sigma_dih(k,i)=0.0
+ cycle
+ endif
+ dih(k,i)=phiref(i) ! right?
+c read (ientin,*) sigma_dih(k,i) ! original variant
+c write (iout,*) "dih(",k,i,") =",dih(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
+c & "rescore(",k,i-1,") =",rescore(k,i-1),
+c & "rescore(",k,i-2,") =",rescore(k,i-2),
+c & "rescore(",k,i-3,") =",rescore(k,i-3)
+
+ sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2)+rescore(k,i-3))/4.0
+c if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
+c write (iout,*) "Raw sigmas for dihedral angle restraints"
+c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
+c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
+c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
+c Instead of res sim other local measure of b/b str reliability possible
+ if (sigma_dih(k,i).ne.0)
+ & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
+ enddo
+ lim_dih=nct-nnt-2
+ endif
+
+ if (waga_theta.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_theta,status='old')
+c do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
+c read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
+c sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_theta(k,i+nnt-1)
+c enddo
+c1403 continue
+c close (ientin)
+
+ do i = nnt+2,nct ! right? without parallel.
+c do i = i=1,nres ! alternative for bounds acc to readpdb?
+c do i=ithet_start,ithet_end ! with FG parallel.
+ if (idomain(k,i).eq.0) then
+ sigma_theta(k,i)=0.0
+ cycle
+ endif
+ thetatpl(k,i)=thetaref(i)
+c write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
+c & "rescore(",k,i-1,") =",rescore(k,i-1),
+c & "rescore(",k,i-2,") =",rescore(k,i-2)
+c read (ientin,*) sigma_theta(k,i) ! 1st variant
+ sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2))/3.0
+c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
+ if (sigma_theta(k,i).ne.0)
+ & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+
+c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
+c rescore(k,i-2) ! right expression ?
+c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
+ enddo
+ endif
+
+ if (waga_d.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_d,status='old')
+c do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
+c read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
+c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_d(k,i+nnt-1)
+c enddo
+c1404 continue
+
+ do i = nnt,nct ! right? without parallel.
+c do i=2,nres-1 ! alternative for bounds acc to readpdb?
+c do i=loc_start,loc_end ! with FG parallel.
+ if (itype(i).eq.10) cycle
+ if (idomain(k,i).eq.0 ) then
+ sigma_d(k,i)=0.0
+ cycle
+ endif
+ xxtpl(k,i)=xxref(i)
+ yytpl(k,i)=yyref(i)
+ zztpl(k,i)=zzref(i)
+c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
+c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
+c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
+ sigma_d(k,i)=rescore(k,i) ! right expression ?
+ if (sigma_d(k,i).ne.0)
+ & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+
+c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
+c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
+c read (ientin,*) sigma_d(k,i) ! 1st variant
+ if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
+ enddo
+ endif
+ enddo
+c
+c remove distance restraints not used in any model from the list
+c shift data in all arrays
+c
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ liiflag=.true.
+ do i=nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ if (ii_in_use(ii).eq.0.and.liiflag) then
+ liiflag=.false.
+ iistart=ii
+ endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag.or.
+ & .not.liiflag.and.ii.eq.lim_odl) then
+ if (ii.eq.lim_odl) then
+ iishift=ii-iistart+1
+ else
+ iishift=ii-iistart
+ endif
+ liiflag=.true.
+ do ki=iistart,lim_odl-iishift
+ ires_homo(ki)=ires_homo(ki+iishift)
+ jres_homo(ki)=jres_homo(ki+iishift)
+ ii_in_use(ki)=ii_in_use(ki+iishift)
+ do k=1,constr_homology
+ odl(k,ki)=odl(k,ki+iishift)
+ sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
+ l_homo(k,ki)=l_homo(k,ki+iishift)
+ enddo
+ enddo
+ ii=ii-iishift
+ lim_odl=lim_odl-iishift
+ endif
+ enddo
+ enddo
+ endif
+
+ endif ! .not. klapaucjusz
+
+ if (constr_homology.gt.0) call homology_partition
+ if (constr_homology.gt.0) call init_int_table
+cd write (iout,*) "homology_partition: lim_theta= ",lim_theta,
+cd & "lim_xx=",lim_xx
+c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
+c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
+c
+c Print restraints
+c
+ if (.not.lprn) return
+cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write (iout,*) "Distance restraints from templates"
+ do ii=1,lim_odl
+ write(iout,'(3i5,100(2f8.2,1x,l1,4x))')
+ & ii,ires_homo(ii),jres_homo(ii),
+ & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii),
+ & ki=1,constr_homology)
+ enddo
+ write (iout,*) "Dihedral angle restraints from templates"
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*dih(ki,i),
+ & rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
+ enddo
+ write (iout,*) "Virtual-bond angle restraints from templates"
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*thetatpl(ki,i),
+ & rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
+ enddo
+ write (iout,*) "SC restraints from templates"
+ do i=nnt,nct
+ write(iout,'(i5,100(4f8.2,4x))') i,
+ & (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
+ & 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
+ enddo
+ endif
+c -----------------------------------------------------------------
+ return
+ end
+c -----------------------------------------------------------------
+ subroutine read_klapaucjusz
+
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.MD'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ character*256 fragfile
+ integer ninclust(maxclust),inclust(max_template,maxclust),
+ & nresclust(maxclust),iresclust(maxres,maxclust)
+
+ character*2 kic2
+ character*24 model_ki_dist, model_ki_angle
+ character*500 controlcard
+ integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
+ logical lprn /.true./
+ integer ilen
+ external ilen
+ logical liiflag
+c
+c
+ double precision rescore_tmp,x12,y12,z12,rescore2_tmp
+ double precision, dimension (max_template,maxres) :: rescore
+ double precision, dimension (max_template,maxres) :: rescore2
+ character*24 pdbfile,tpl_k_rescore
+
+c
+c For new homol impl
+c
+ include 'COMMON.VAR'
+c
+ call getenv("FRAGFILE",fragfile)
+ open(ientin,file=fragfile,status="old",err=10)
+ read(ientin,*) constr_homology,nclust
+ l_homo = .false.
+ sigma_theta=0.0
+ sigma_d=0.0
+ sigma_dih=0.0
+c Read pdb files
+ do k=1,constr_homology
+ read(ientin,'(a)') pdbfile
+ write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ open(ipdbin,file=pdbfile,status='old',err=33)
+ goto 34
+ 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ stop
+ 34 continue
+ unres_pdb=.false.
+ call readpdb_template(k)
+ do i=1,nres
+ rescore(k,i)=1.0d0
+ rescore2(k,i)=1.0d0
+ enddo
+ enddo
+c Read clusters
+ do i=1,nclust
+ read(ientin,*) ninclust(i),nresclust(i)
+ read(ientin,*) (inclust(k,i),k=1,ninclust(i))
+ read(ientin,*) (iresclust(k,i),k=1,nresclust(i))
+ enddo
+c
+c Loop over clusters
+c
+ do l=1,nclust
+ do ll = 1,ninclust(l)
+
+ k = inclust(ll,l)
+ do i=1,nres
+ idomain(k,i)=0
+ enddo
+ do i=1,nresclust(l)
+ if (nnt.gt.1) then
+ idomain(k,iresclust(i,l)+1) = 1
+ else
+ idomain(k,iresclust(i,l)) = 1
+ endif
+ enddo
+c
+c Distance restraints
+c
+c ... --> odl(k,ii)
+C Copy the coordinates from reference coordinates (?)
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=chomo(j,i,k)
+c write (iout,*) "c(",j,i,") =",c(j,i)
+ enddo
+ enddo
+ call int_from_cart(.true.,.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ enddo
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+
+ x12=c(1,i)-c(1,j)
+ y12=c(2,i)-c(2,j)
+ z12=c(3,i)-c(3,j)
+ distal=dsqrt(x12*x12+y12*y12+z12*z12)
+c write (iout,*) k,i,j,distal,dist2_cut
+
+ if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+ & .and. distal.le.dist2_cut ) then
+
+ ii=ii+1
+ ii_in_use(ii)=1
+ l_homo(k,ii)=.true.
+
+c write (iout,*) "k",k
+c write (iout,*) "i",i," j",j," constr_homology",
+c & constr_homology
+ ires_homo(ii)=i
+ jres_homo(ii)=j
+ odl(k,ii)=distal
+ if (read2sigma) then
+ sigma_odl(k,ii)=0
+ do ik=i,j
+ sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
+ enddo
+ sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
+ if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
+ & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+ else
+ if (odl(k,ii).le.dist_cut) then
+ sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
+ else
+#ifdef OLDSIGMA
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
+#else
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+#endif
+ endif
+ endif
+ sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
+ else
+ ii=ii+1
+c l_homo(k,ii)=.false.
+ endif
+ enddo
+ enddo
+ lim_odl=ii
+ endif
+c
+c Theta, dihedral and SC retraints
+c
+ if (waga_angle.gt.0.0d0) then
+ do i = nnt+3,nct
+ if (idomain(k,i).eq.0) then
+c sigma_dih(k,i)=0.0
+ cycle
+ endif
+ dih(k,i)=phiref(i)
+ sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2)+rescore(k,i-3))/4.0
+c write (iout,*) "k",k," l",l," i",i," rescore",rescore(k,i),
+c & " sigma_dihed",sigma_dih(k,i)
+ if (sigma_dih(k,i).ne.0)
+ & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+ enddo
+ lim_dih=nct-nnt-2
+ endif
+
+ if (waga_theta.gt.0.0d0) then
+ do i = nnt+2,nct
+ if (idomain(k,i).eq.0) then
+c sigma_theta(k,i)=0.0
+ cycle
+ endif
+ thetatpl(k,i)=thetaref(i)
+ sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2))/3.0
+ if (sigma_theta(k,i).ne.0)
+ & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+ enddo
+ endif
+
+ if (waga_d.gt.0.0d0) then
+ do i = nnt,nct
+ if (itype(i).eq.10) cycle
+ if (idomain(k,i).eq.0 ) then
+c sigma_d(k,i)=0.0
+ cycle
+ endif
+ xxtpl(k,i)=xxref(i)
+ yytpl(k,i)=yyref(i)
+ zztpl(k,i)=zzref(i)
+ sigma_d(k,i)=rescore(k,i)
+ if (sigma_d(k,i).ne.0)
+ & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+ if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1
+ enddo
+ endif
+ enddo ! l
+ enddo ! ll
+c
+c remove distance restraints not used in any model from the list
+c shift data in all arrays
+c
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ liiflag=.true.
+ do i=nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ if (ii_in_use(ii).eq.0.and.liiflag) then
+ liiflag=.false.
+ iistart=ii
+ endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag.or.
+ & .not.liiflag.and.ii.eq.lim_odl) then
+ if (ii.eq.lim_odl) then
+ iishift=ii-iistart+1
+ else
+ iishift=ii-iistart
+ endif
+ liiflag=.true.
+ do ki=iistart,lim_odl-iishift
+ ires_homo(ki)=ires_homo(ki+iishift)
+ jres_homo(ki)=jres_homo(ki+iishift)
+ ii_in_use(ki)=ii_in_use(ki+iishift)
+ do k=1,constr_homology
+ odl(k,ki)=odl(k,ki+iishift)
+ sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
+ l_homo(k,ki)=l_homo(k,ki+iishift)
+ enddo
+ enddo
+ ii=ii-iishift
+ lim_odl=lim_odl-iishift
+ endif
+ enddo
+ enddo
+ endif
+
+ return
+ 10 stop "Error infragment file"
+ end
+c----------------------------------------------------------------------
+
#ifdef WINIFL
subroutine flush(iu)
return
return
end
#endif
+
c------------------------------------------------------------------------------
subroutine copy_to_tmp(source)
include "DIMENSIONS"
projects / unres.git / blobdiff