X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fcluster%2Fwham%2Fsrc-HCD-5D%2Freadrtns.F;h=a3229a6a437c1e9f67e0003095471e3325bcc917;hb=b6b1679cfe492bd5b73e03410f82917bd9c3aa7b;hp=33ac81aef7d4bfdcac0175a5b5c5d4e43f11ab44;hpb=fb31d9cf50bce06dbfae62c92c11f3e9c836f405;p=unres.git

diff --git a/source/cluster/wham/src-HCD-5D/readrtns.F b/source/cluster/wham/src-HCD-5D/readrtns.F
index 33ac81a..a3229a6 100644
--- a/source/cluster/wham/src-HCD-5D/readrtns.F
+++ b/source/cluster/wham/src-HCD-5D/readrtns.F
@@ -39,8 +39,10 @@ C Reading the dimensions of box in x,y,z coordinates
       call reada(controlcard,'BOXY',boxysize,100.0d0)
       call reada(controlcard,'BOXZ',boxzsize,100.0d0)
 c Cutoff range for interactions
-      call reada(controlcard,"R_CUT",r_cut,15.0d0)
+      call reada(controlcard,"R_CUT",r_cut,25.0d0)
       call reada(controlcard,"LAMBDA",rlamb,0.3d0)
+      write (iout,*) "Cutoff on interactions",r_cut
+      write (iout,*) "lambda",rlamb
       call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
       call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
       if (lipthick.gt.0.0d0) then
@@ -424,6 +426,13 @@ c      print *,'NNT=',NNT,' NCT=',NCT
        print*, 'read_dfa_info finished!'
       endif
 #endif
+C If the reference structure is not read set the superposition
+C boundaries
+      nstart_sup=nnt
+      nstart_seq=nnt
+      nend_sup=nct
+      nsup=nct-nnt+1
+
       if (with_dihed_constr) then
 
       read (inp,*) ndih_constr
@@ -628,48 +637,25 @@ c     &                 ' nstart_seq=',nstart_seq
 c      endif
       call init_int_table
       call setup_var
-      write (iout,*) "molread: REFSTR",refstr
-      if (refstr) then
-        if (.not.pdbref) then
-          call read_angles(inp,*38)
-          goto 39
-   38     write (iout,'(a)') 'Error reading reference structure.'
-#ifdef MPL
-          call mp_stopall(Error_Msg)
-#else
-          stop 'Error reading reference structure'
-#endif
-   39     call chainbuild     
-          nstart_sup=nnt
-          nstart_seq=nnt
-          nsup=nct-nnt+1
-          do i=1,2*nres
-            do j=1,3
-              cref(j,i)=c(j,i)
-            enddo
-          enddo
-        endif
-c        call contact(.true.,ncont_ref,icont_ref)
-      endif
-       if (ns.gt.0) then
-C        write (iout,'(/a,i3,a)')
-C     &  'The chain contains',ns,' disulfide-bridging cysteines.'
+      if (ns.gt.0) then
+C       write (iout,'(/a,i3,a)')
+C       'The chain contains',ns,' disulfide-bridging cysteines.'
         write (iout,'(20i4)') (iss(i),i=1,ns)
-       if (dyn_ss) then
+        if (dyn_ss) then
           write(iout,*)"Running with dynamic disulfide-bond formation"
-       else
-        write (iout,'(/a/)') 'Pre-formed links are:'
-        do i=1,nss
-          i1=ihpb(i)-nres
-          i2=jhpb(i)-nres
-          it1=itype(i1)
-          it2=itype(i2)
-          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
+        else
+          write (iout,'(/a/)') 'Pre-formed links are:'
+          do i=1,nss
+            i1=ihpb(i)-nres
+            i2=jhpb(i)-nres
+            it1=itype(i1)
+            it2=itype(i2)
+            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