X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=sidebyside;f=source%2Funres%2Fsrc_MD%2Freadrtns.F;h=5b74f874d9c470a0f146b83d5f54bff5ea61f5ef;hb=87128dda6cd087e5baee8bfe7453c2d9c879fa54;hp=4c1e4b9e9e3c85cab3805336973d714b432d05df;hpb=cc6bfed2a73175fb7329acdd60f3d89d9f25afbb;p=unres.git

diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index 4c1e4b9..5b74f87 100644
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -893,6 +893,9 @@ c        print *,'Finished reading pdb data'
         call contact(.false.,ncont_ref,icont_ref,co)
 
         if (sideadd) then 
+C Following 2 lines for diagnostics; comment out if not needed
+         write (iout,*) "Before sideadd"
+         call intout
          if(me.eq.king.or..not.out1file)
      &    write(iout,*)'Adding sidechains'
          maxsi=1000
@@ -909,7 +912,12 @@ c        print *,'Finished reading pdb data'
      &              i,' after ',nsi,' trials'
           endif
          enddo
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+         call chainbuild
         endif  
+C Following 2 lines for diagnostics; comment out if not needed
+        write (iout,*) "After sideadd"
+        call intout
       endif
       if (indpdb.eq.0) then
 C Read sequence if not taken from the pdb file.
@@ -930,8 +938,8 @@ C Assign initial virtual bond lengths
           vbld_inv(i)=vblinv
         enddo
         do i=2,nres-1
-          vbld(i+nres)=dsc(iabs(itype(i)))
-          vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
+          vbld(i+nres)=dsc(itype(i))
+          vbld_inv(i+nres)=dsc_inv(itype(i))
 c          write (iout,*) "i",i," itype",itype(i),
 c     &      " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
         enddo
@@ -1095,8 +1103,8 @@ czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
 c        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
       if (constr_dist.gt.0) then
         call read_dist_constr
-        call hpb_partition
       endif
+      if (nhpb.gt.0) call hpb_partition
 c      write (iout,*) "After read_dist_constr nhpb",nhpb
 c      call flush(iout)
       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
@@ -1151,7 +1159,6 @@ C initial geometry.
          enddo
          do i=2,nres-1
           omeg(i)=-120d0*deg2rad
-          if (itype(i).le.0) omeg(i)=-omeg(i)
          enddo
         else
           if(me.eq.king.or..not.out1file)