X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Freadrtns.F;h=509361d932f91dd7d9ffa98c8493db3dca9b0429;hb=aa4540154949fdfc9ab63442eb6fea09d6c589ad;hp=056bfd43c91cba638c14e21ae33bc7310187ed72;hpb=c3d632cf84fd647434c093cb3fd69ea605293f75;p=unres.git diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F index 056bfd4..509361d 100644 --- a/source/unres/src_MD/readrtns.F +++ b/source/unres/src_MD/readrtns.F @@ -8,6 +8,7 @@ include 'COMMON.CONTROL' include 'COMMON.SBRIDGE' include 'COMMON.IOUNITS' + include 'COMMON.CHAIN' logical file_exist C Read force-field parameters except weights call parmread @@ -130,6 +131,7 @@ C Set up the time limit (caution! The time must be input in 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) @@ -386,6 +388,11 @@ C 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 @@ -426,6 +433,10 @@ c if performing umbrella sampling, fragments constrained are read from the frag 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 @@ -627,6 +638,7 @@ C common /pizda/ itype_pdb logical seq_comp,fail double precision energia(0:n_ene) + integer ilen external ilen C @@ -922,6 +934,17 @@ C 12/1/95 Added weight for the multi-body term WCORR 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, @@ -1165,6 +1188,44 @@ c write (iout,*) "constr_dist",constr_dist,nstart_sup,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 @@ -1182,6 +1243,8 @@ C initial geometry. 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) @@ -1200,7 +1263,7 @@ C initial geometry. enddo endif enddo - return +c return else call read_angles(inp,*36) endif @@ -1284,6 +1347,8 @@ C Generate distance constraints, if the PDB structure is to be regularized. 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 @@ -2262,6 +2327,8 @@ c print *,"Processor",myrank," fg_rank",fg_rank & //'.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) @@ -2280,6 +2347,7 @@ c print *,"Processor",myrank," fg_rank",fg_rank 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) @@ -2440,33 +2508,36 @@ c------------------------------------------------------------------------------- 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 @@ -2672,22 +2743,21 @@ c Alternative: reading from input 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 @@ -2734,6 +2804,7 @@ c tpl_k_sigma_dih="template"//kic2//".sigma_dih" 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 @@ -2773,7 +2844,7 @@ c & sigma_odl_temp(i+nnt-1,j+nnt-1,k) 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? @@ -2813,8 +2884,13 @@ c sigma_odl(k,ii)=rescore(k,i)+rescore(k,j) ! other exprs possible c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j) else +#ifdef OLDSIGMA sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error & dexp(0.5d0*(odl(k,ii)/dist_cut)**2) +#else + sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error + & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0) +#endif c Following expr replaced by a positive exp argument c sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* @@ -2938,40 +3014,41 @@ c read (ientin,*) sigma_d(k,i) ! 1st variant 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