include 'COMMON.CONTROL'
include 'COMMON.SBRIDGE'
include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
logical file_exist
C Read force-field parameters except weights
call parmread
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)
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
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,
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(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
& //'.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.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,"HOMOL_NSET",homol_nset,1)
if (homol_nset.gt.1)then
call card_concat(controlcard)
- read(controlcard,*) (waga_dist1(i),i=1,homol_nset)
- call card_concat(controlcard)
- read(controlcard,*) (waga_angle1(i),i=1,homol_nset)
- write(iout,*) "iset distance_weight angle_weight"
- do i=1,homol_nset
- write(iout,*) i,waga_dist1(i),waga_angle1(i)
- enddo
+ 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
-c call reada(controlcard,"HOMOL_DIST",waga_dist(1),1.0d0)
-c call reada(controlcard,"HOMOL_ANGLE",waga_angle(1),1.0d0)
+ waga_homology(1)=1.0
endif
- write (iout,*) "nnt",nnt," nct",nct
- call flush(iout)
+cd write (iout,*) "nnt",nnt," nct",nct
+cd call flush(iout)
lim_odl=0
c tpl_k_sigma_theta="template"//kic2//".sigma_theta"
c tpl_k_sigma_d="template"//kic2//".sigma_d"
+ unres_pdb=.false.
call readpdb
c
c Distance restraints
c enddo
c 1401 continue
c close (ientin)
- if (waga_dist.gt.0.0d0) then
+ if (waga_dist.ne.0.0d0) then
ii=0
do i = nnt,nct-2 ! right? without parallel.
do j=i+2,nct ! right?
endif
close(ientin)
enddo
- if (waga_dist.gt.0.0d0) lim_odl=ii
+ if (waga_dist.ne.0.0d0) lim_odl=ii
if (constr_homology.gt.0) call homology_partition
if (constr_homology.gt.0) call init_int_table
- write (iout,*) "homology_partition: lim_theta= ",lim_theta,
- & "lim_xx=",lim_xx
+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
- write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
- write (iout,*) "Distance restraints from templates"
- do ii=1,lim_odl
+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,'(3i5,10(2f16.2,4x))') ii,ires_homo(ii),jres_homo(ii),
& (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),ki=1,constr_homology)
- enddo
- write (iout,*) "Dihedral angle restraints from templates"
- do i=nnt+3,lim_dih
+ enddo
+ write (iout,*) "Dihedral angle restraints from templates"
+ do i=nnt+3,lim_dih
write (iout,'(i5,10(2f8.2,4x))') 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,lim_theta
+ enddo
+ write (iout,*) "Virtual-bond angle restraints from templates"
+ do i=nnt+2,lim_theta
write (iout,'(i5,10(2f8.2,4x))') 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,lim_xx
+ enddo
+ write (iout,*) "SC restraints from templates"
+ do i=nnt,lim_xx
write(iout,'(i5,10(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
-
+ enddo
+ endif
c -----------------------------------------------------------------
return
end
projects / unres.git / blobdiff