From dd7bdb2c09f0c456056e31ef2eedb894d1f0e92c Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Fri, 22 May 2020 23:29:09 +0200 Subject: [PATCH] cluster & wham update --- source/cluster/wham/src-HCD/COMMON.CHAIN | 5 +- source/cluster/wham/src-HCD/energy_p_new.F | 1 + source/cluster/wham/src-HCD/read_constr_homology.F | 105 +++++++++++------- source/cluster/wham/src-HCD/readpdb.F | 23 ++-- source/wham/src-HCD/COMMON.CHAIN | 5 +- source/wham/src-HCD/energy_p_new.F | 1 - source/wham/src-HCD/read_constr_homology.F | 115 +++++++++++++------- source/wham/src-HCD/readpdb.F | 6 +- 8 files changed, 168 insertions(+), 93 deletions(-) diff --git a/source/cluster/wham/src-HCD/COMMON.CHAIN b/source/cluster/wham/src-HCD/COMMON.CHAIN index 9de64dd..2b481a5 100644 --- a/source/cluster/wham/src-HCD/COMMON.CHAIN +++ b/source/cluster/wham/src-HCD/COMMON.CHAIN @@ -1,6 +1,6 @@ integer nres,nres0,nsup,nstart_sup,nend_sup,nstart_seq, & nchain,chain_border,chain_length,ireschain,npermchain, - & tabpermchain,ishift_pdb,iz_sc + & tabpermchain,ishift_pdb,iz_sc,nres_chomo double precision c,cref,crefjlee,cref_pdb,dc,xloc,xrot,dc_norm, & t,r,prod,rt,chomo common /chain/ c(3,maxres2+2),dc(3,maxres2),xloc(3,maxres), @@ -18,4 +18,5 @@ & buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick common /box/ boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad, & buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick - common /chomo_models/ chomo(3,maxres2+2,max_template) + common /chomo_models/ chomo(3,maxres2+2,max_template), + & nres_chomo(max_template) diff --git a/source/cluster/wham/src-HCD/energy_p_new.F b/source/cluster/wham/src-HCD/energy_p_new.F index 95898b4..5d07d5d 100644 --- a/source/cluster/wham/src-HCD/energy_p_new.F +++ b/source/cluster/wham/src-HCD/energy_p_new.F @@ -10217,6 +10217,7 @@ c min_odl=minval(distancek) & min_odl=distancek(kk) enddo endif + c write (iout,* )"min_odl",min_odl #ifdef DEBUG write (iout,*) "ij dij",i,j,dij diff --git a/source/cluster/wham/src-HCD/read_constr_homology.F b/source/cluster/wham/src-HCD/read_constr_homology.F index b188deb..6ae3ef4 100644 --- a/source/cluster/wham/src-HCD/read_constr_homology.F +++ b/source/cluster/wham/src-HCD/read_constr_homology.F @@ -1,5 +1,5 @@ subroutine read_constr_homology - + implicit none include 'DIMENSIONS' #ifdef MPI include 'mpif.h' @@ -27,16 +27,19 @@ 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 + integer ki,i,ii,ik,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp, + & lim_theta,lim_xx,irec,iistart,iishift,i10,i01 + double precision distal integer idomain(max_template,maxres) - logical lprn /.true./ + logical lfirst integer ilen external ilen logical liiflag + integer nres_temp c c FP - Nov. 2014 Temporary specifications for new vars c - double precision rescore_tmp,x12,y12,z12,rescore2_tmp + double precision rescore_tmp,x12,y12,z12,rescore2_tmp, & rescore3_tmp double precision, dimension (max_template,maxres) :: rescore double precision, dimension (max_template,maxres) :: rescore2 @@ -142,6 +145,7 @@ c tpl_k_rescore="template"//kic2//".sco" unres_pdb=.false. + nres_temp=nres if (read2sigma) then call readpdb_template(k) close(ipdbin) @@ -149,15 +153,16 @@ c call readpdb(out_template_coord) close(ipdbin) endif + nres_chomo(k)=nres + nres=nres_temp -c 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 + do i=1,nres_chomo(k) write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3), & (crefjlee(j,i+nres),j=1,3) enddo @@ -170,7 +175,7 @@ c Distance restraints c c ... --> odl(k,ii) C Copy the coordinates from reference coordinates (?) - do i=1,2*nres + do i=1,2*nres_chomo(k) do j=1,3 c(j,i)=cref(j,i) c write (iout,*) "c(",j,i,") =",c(j,i) @@ -259,6 +264,8 @@ c & constr_homology enddo lim_odl=ii endif +c write (iout,*) "Distance restraints set" +c call flush(iout) c c Theta, dihedral and SC retraints c @@ -294,11 +301,13 @@ 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)) + & 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 +c write (iout,*) "Dihedral angle restraints set" +c call flush(iout) if (waga_theta.gt.0.0d0) then c open (ientin,file=tpl_k_sigma_theta,status='old') @@ -334,6 +343,8 @@ c rescore(k,i-2) ! right expression ? c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i) enddo endif +c write (iout,*) "Angle restraints set" +c call flush(iout) if (waga_d.gt.0.0d0) then c open (ientin,file=tpl_k_sigma_d,status='old') @@ -359,7 +370,6 @@ 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) -c sigma_d(k,i)=rescore(k,i) ! right expression ? sigma_d(k,i)=rescore3(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)) @@ -370,57 +380,70 @@ c read (ientin,*) sigma_d(k,i) ! 1st variant enddo endif enddo +c write (iout,*) "SC restraints set" +c call flush(iout) c c remove distance restraints not used in any model from the list c shift data in all arrays c +c write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct if (waga_dist.ne.0.0d0) then ii=0 liiflag=.true. + lfirst=.true. do i=nnt,nct-2 do j=i+2,nct ii=ii+1 - if (ii_in_use(ii).eq.0.and.liiflag) then +c if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0 +c & .and. distal.le.dist2_cut ) then +c write (iout,*) "i",i," j",j," ii",ii +c call flush(iout) + if (ii_in_use(ii).eq.0.and.liiflag.or. + & ii_in_use(ii).eq.1.and.liiflag.and.ii.eq.lim_odl) then liiflag=.false. - iistart=ii + i10=ii + if (lfirst) then + lfirst=.false. + iistart=ii + else + if(i10.eq.lim_odl) i10=i10+1 + do ki=0,i10-i01-1 + ires_homo(iistart+ki)=ires_homo(ki+i01) + jres_homo(iistart+ki)=jres_homo(ki+i01) + ii_in_use(iistart+ki)=ii_in_use(ki+i01) + do k=1,constr_homology + odl(k,iistart+ki)=odl(k,ki+i01) + sigma_odl(k,iistart+ki)=sigma_odl(k,ki+i01) + l_homo(k,iistart+ki)=l_homo(k,ki+i01) + enddo + enddo + iistart=iistart+i10-i01 + endif 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 + if (ii_in_use(ii).ne.0.and..not.liiflag) then + i01=ii 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 + lim_odl=iistart-1 endif - - endif ! .not. klapaucjusz +c write (iout,*) "Removing distances completed" +c call flush(iout) + endif ! .not. klapaucjusz if (constr_homology.gt.0) call homology_partition +c write (iout,*) "After homology_partition" +c call flush(iout) 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 write (iout,*) "After init_int_table" +c call flush(iout) +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 + if (.not.out_template_restr) return cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then write (iout,*) "Distance restraints from templates" @@ -477,7 +500,9 @@ c---------------------------------------------------------------------- character*500 controlcard integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp integer idomain(max_template,maxres) + integer nres_temp logical lprn /.true./ + logical lfirst integer ilen external ilen logical liiflag @@ -513,7 +538,10 @@ c Read pdb files stop 34 continue unres_pdb=.false. + nres_temp=nres call readpdb_template(k) + nres_chomo(k)=nres + nres=nres_temp c do i=1,2*nres c do j=1,3 c chomo(j,i,k)=c(j,i) @@ -552,6 +580,8 @@ c Distance restraints c c ... --> odl(k,ii) C Copy the coordinates from reference coordinates (?) + nres_temp=nres + nres=nres_chomo(k) do i=1,2*nres do j=1,3 c(j,i)=chomo(j,i,k) @@ -564,6 +594,7 @@ c write (iout,*) "c(",j,i,") =",c(j,i) thetaref(i)=theta(i) phiref(i)=phi(i) enddo + nres=nres_temp if (waga_dist.ne.0.0d0) then ii=0 do i = nnt,nct-2 diff --git a/source/cluster/wham/src-HCD/readpdb.F b/source/cluster/wham/src-HCD/readpdb.F index a7bb52b..58c63e4 100644 --- a/source/cluster/wham/src-HCD/readpdb.F +++ b/source/cluster/wham/src-HCD/readpdb.F @@ -98,7 +98,7 @@ c write (2,'(a)') card ! write (iout,*) "Calculating sidechain center iii",iii if (unres_pdb) then do j=1,3 - dc(j,ires+nres)=sccor(j,iii) + dc(j,ires_old)=sccor(j,iii) enddo else call sccenter(ires_old,iii,sccor) @@ -347,17 +347,20 @@ c character*5 atom & ' Gamma' endif endif - do i=1,nres-1 + do i=2,nres iti=itype(i) - if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then +c write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1) + if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and. + & (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then write (iout,'(a,i4)') 'Bad Cartesians for residue',i -ctest stop +c stop endif - vbld(i+1)=dist(i,i+1) - vbld_inv(i+1)=1.0d0/vbld(i+1) - if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1) + vbld(i)=dist(i-1,i) + vbld_inv(i)=1.0d0/vbld(i) + theta(i+1)=alpha(i-1,i,i+1) if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1) enddo + c if (unres_pdb) then c if (itype(1).eq.ntyp1) then c theta(3)=90.0d0*deg2rad @@ -806,7 +809,7 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue endif endif C Calculate internal coordinates. - if (lprn) then + if (out_template_coord) then write (iout,'(/a)') & "Cartesian coordinates of the reference structure" write (iout,'(a,3(3x,a5),5x,3(3x,a5))') @@ -818,6 +821,7 @@ C Calculate internal coordinates. enddo endif C Calculate internal coordinates. +#ifdef DEBUG write (iout,'(a)') & "Backbone and SC coordinates as read from the PDB" do ires=1,nres @@ -825,7 +829,8 @@ C Calculate internal coordinates. & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3), & (c(j,nres+ires),j=1,3) enddo - call int_from_cart(.true.,.false.) +#endif + call int_from_cart(.true.,out_template_coord) call sc_loc_geom(.false.) do i=1,nres thetaref(i)=theta(i) diff --git a/source/wham/src-HCD/COMMON.CHAIN b/source/wham/src-HCD/COMMON.CHAIN index dfffc78..7b79a58 100644 --- a/source/wham/src-HCD/COMMON.CHAIN +++ b/source/wham/src-HCD/COMMON.CHAIN @@ -1,6 +1,6 @@ integer nres,nres0,nsup,nstart_sup,nend_sup,nstart_seq, & ishift_pdb,chain_length,chain_border,chain_border1,ichanres, - & tabpermchain,nchain ,npermchain,ireschain,iz_sc + & tabpermchain,nchain ,npermchain,ireschain,iz_sc,nres_chomo double precision c,cref,crefjlee,dc,xloc,xrot,dc_norm,t,r,prod,rt, & rmssing,anatemp,chomo common /chain/ c(3,maxres2+2),dc(3,maxres2),xloc(3,maxres), @@ -18,4 +18,5 @@ & buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick common /box/ boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad, & buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick - common /chomo_models/ chomo(3,maxres2+2,max_template) + common /chomo_models/ chomo(3,maxres2+2,max_template), + & nres_chomo(max_template) diff --git a/source/wham/src-HCD/energy_p_new.F b/source/wham/src-HCD/energy_p_new.F index efba869..6105156 100644 --- a/source/wham/src-HCD/energy_p_new.F +++ b/source/wham/src-HCD/energy_p_new.F @@ -159,7 +159,6 @@ c write (iout,*) "Calling multibody_hbond" call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1) endif #endif -c write (iout,*) "nsaxs",nsaxs c write (iout,*) "From Esaxs: Esaxs_constr",Esaxs_constr if (nsaxs.gt.0 .and. saxs_mode.eq.0) then call e_saxs(Esaxs_constr) diff --git a/source/wham/src-HCD/read_constr_homology.F b/source/wham/src-HCD/read_constr_homology.F index 0af2bdb..fa81b80 100644 --- a/source/wham/src-HCD/read_constr_homology.F +++ b/source/wham/src-HCD/read_constr_homology.F @@ -1,5 +1,6 @@ subroutine read_constr_homology + implicit none include 'DIMENSIONS' include 'DIMENSIONS.ZSCOPT' include 'DIMENSIONS.FREE' @@ -29,12 +30,15 @@ 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 + integer ki,i,ii,ik,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp, + & lim_theta,lim_xx,irec,iistart,iishift,i10,i01 + double precision distal integer idomain(max_template,maxres) - logical lprn /.true./ + logical lfirst integer ilen external ilen logical liiflag + integer nres_temp c c FP - Nov. 2014 Temporary specifications for new vars c @@ -143,6 +147,7 @@ c tpl_k_rescore="template"//kic2//".sco" unres_pdb=.false. + nres_temp=nres if (read2sigma) then call readpdb_template(k) close(ipdbin) @@ -150,15 +155,16 @@ c call readpdb close(ipdbin) endif + nres_chomo(k)=nres + nres=nres_temp -c call readpdb - do i=1,2*nres + do i=1,2*nres_chomo(k) do j=1,3 crefjlee(j,i)=c(j,i) enddo enddo #ifdef DEBUG - do i=1,nres + do i=1,nres_chmo(k) write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3), & (crefjlee(j,i+nres),j=1,3) enddo @@ -171,7 +177,7 @@ c Distance restraints c c ... --> odl(k,ii) C Copy the coordinates from reference coordinates (?) - do i=1,2*nres + do i=1,2*nres_chomo(k) do j=1,3 c(j,i)=cref(j,i) c write (iout,*) "c(",j,i,") =",c(j,i) @@ -260,6 +266,8 @@ c & constr_homology enddo lim_odl=ii endif +c write (iout,*) "Distance restraints set" +c call flush(iout) c c Theta, dihedral and SC retraints c @@ -295,11 +303,13 @@ 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)) + & 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 +c write (iout,*) "Dihedral angle restraints set" +c call flush(iout) if (waga_theta.gt.0.0d0) then c open (ientin,file=tpl_k_sigma_theta,status='old') @@ -335,6 +345,8 @@ c rescore(k,i-2) ! right expression ? c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i) enddo endif +c write (iout,*) "Angle restraints set" +c call flush(iout) if (waga_d.gt.0.0d0) then c open (ientin,file=tpl_k_sigma_d,status='old') @@ -360,7 +372,6 @@ 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) -c sigma_d(k,i)=rescore(k,i) ! right expression ? sigma_d(k,i)=rescore3(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)) @@ -371,57 +382,70 @@ c read (ientin,*) sigma_d(k,i) ! 1st variant enddo endif enddo +c write (iout,*) "SC restraints set" +c call flush(iout) c c remove distance restraints not used in any model from the list c shift data in all arrays c +c write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct if (waga_dist.ne.0.0d0) then ii=0 liiflag=.true. + lfirst=.true. do i=nnt,nct-2 do j=i+2,nct ii=ii+1 - if (ii_in_use(ii).eq.0.and.liiflag) then +c if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0 +c & .and. distal.le.dist2_cut ) then +c write (iout,*) "i",i," j",j," ii",ii +c call flush(iout) + if (ii_in_use(ii).eq.0.and.liiflag.or. + & ii_in_use(ii).eq.1.and.liiflag.and.ii.eq.lim_odl) then liiflag=.false. - iistart=ii + i10=ii + if (lfirst) then + lfirst=.false. + iistart=ii + else + if(i10.eq.lim_odl) i10=i10+1 + do ki=0,i10-i01-1 + ires_homo(iistart+ki)=ires_homo(ki+i01) + jres_homo(iistart+ki)=jres_homo(ki+i01) + ii_in_use(iistart+ki)=ii_in_use(ki+i01) + do k=1,constr_homology + odl(k,iistart+ki)=odl(k,ki+i01) + sigma_odl(k,iistart+ki)=sigma_odl(k,ki+i01) + l_homo(k,iistart+ki)=l_homo(k,ki+i01) + enddo + enddo + iistart=iistart+i10-i01 + endif 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 + if (ii_in_use(ii).ne.0.and..not.liiflag) then + i01=ii 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 + lim_odl=iistart-1 endif - - endif ! .not. klapaucjusz +c write (iout,*) "Removing distances completed" +c call flush(iout) + endif ! .not. klapaucjusz if (constr_homology.gt.0) call homology_partition +c write (iout,*) "After homology_partition" +c call flush(iout) 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 write (iout,*) "After init_int_table" +c call flush(iout) +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 + if (.not.out_template_restr) return cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then write (iout,*) "Distance restraints from templates" @@ -455,7 +479,7 @@ c ----------------------------------------------------------------- end c---------------------------------------------------------------------- subroutine read_klapaucjusz - + implicit none include 'DIMENSIONS' include 'DIMENSIONS.ZSCOPT' include 'DIMENSIONS.FREE' @@ -478,8 +502,11 @@ c---------------------------------------------------------------------- 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 + integer i,ii,ik,ki,j,k,l,ll,ii_in_use(maxdim),i_tmp,idomain_tmp, + & nclust,iistart,iishift,lim_xx + integer nres_temp integer idomain(max_template,maxres) + double precision distal logical lprn /.true./ integer ilen external ilen @@ -499,6 +526,7 @@ c call getenv("FRAGFILE",fragfile) open(ientin,file=fragfile,status="old",err=10) read(ientin,*) constr_homology,nclust + lim_xx=0 l_homo = .false. sigma_theta=0.0 sigma_d=0.0 @@ -515,7 +543,10 @@ c Read pdb files stop 34 continue unres_pdb=.false. + nres_temp=nres call readpdb_template(k) + nres_chomo(k)=nres + nres=nres_temp c do i=1,2*nres c do j=1,3 c chomo(j,i,k)=c(j,i) @@ -536,6 +567,7 @@ c c Loop over clusters c do l=1,nclust +c write (iout,*) "CLUSTER",l," members:",ninclust(l) do ll = 1,ninclust(l) k = inclust(ll,l) @@ -555,14 +587,18 @@ c c ... --> odl(k,ii) C Copy the coordinates from reference coordinates (?) c write (iout,*) "k",k + nres_temp=nres + nres=nres_chomo(k) 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 -c call cartprint c write (iout,*) "read_klapaucjusz: calling int_from_cart" +c call cartprint +c write (iout,*) "idomain" +c write (iout,'(2i5)') (i,idomain(k,i),i=1,nres) call int_from_cart(.true.,.false.) call sc_loc_geom(.false.) c write (iout,*) "en" @@ -570,6 +606,7 @@ c write (iout,*) "en" thetaref(i)=theta(i) phiref(i)=phi(i) enddo + nres=nres_temp if (waga_dist.ne.0.0d0) then ii=0 do i = nnt,nct-2 diff --git a/source/wham/src-HCD/readpdb.F b/source/wham/src-HCD/readpdb.F index 55dcc04..6f4ba5f 100644 --- a/source/wham/src-HCD/readpdb.F +++ b/source/wham/src-HCD/readpdb.F @@ -91,7 +91,7 @@ c write (2,'(a)') card ! write (iout,*) "Calculating sidechain center iii",iii if (unres_pdb) then do j=1,3 - dc(j,ires+nres)=sccor(j,iii) + dc(j,ires_old)=sccor(j,iii) enddo else call sccenter(ires_old,iii,sccor) @@ -804,8 +804,8 @@ C Calculate internal coordinates. endif C Calculate internal coordinates. c call int_from_cart1(.false.) - call int_from_cart(.true.,.true.) - call sc_loc_geom(.true.) + call int_from_cart(.true.,out_template_coord) + call sc_loc_geom(.false.) do i=1,nres thetaref(i)=theta(i) phiref(i)=phi(i) -- 1.7.9.5