X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Freadrtns.F;h=b731cf28414c43f932795c94404fde7f533ab1d1;hb=b416cd95f5e18db88f1bba9c9de8cf005a6557f4;hp=c182359801336fb234b60fda12e587306fbcc23b;hpb=04e500c1e6fb2a1882e2871304b3b0721a14c02c;p=unres.git

diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index c182359..b731cf2 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
@@ -928,6 +939,12 @@ c        print *,'Begin reading pdb data'
             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,
@@ -1179,6 +1196,36 @@ c        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
             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
@@ -1196,6 +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)
@@ -1214,7 +1263,7 @@ C initial geometry.
                 enddo
               endif
             enddo
-            return
+c            return
           else
             call read_angles(inp,*36)
           endif
@@ -1298,6 +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
@@ -2276,6 +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)
@@ -2294,6 +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)
@@ -2787,7 +2841,7 @@ 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?
@@ -2952,7 +3006,7 @@ 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
 cd      write (iout,*) "homology_partition: lim_theta= ",lim_theta,