X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fcluster%2Fwham%2Fsrc-HCD-5D%2Freadpdb.F;h=58c63e4208e96b269850edc0953a8c71327e0bc2;hb=79fd686e9d9aaa23e4fda802ee16379470e961d3;hp=a7bb52bfbd5bc493fd051db5cff8c71ece0a3d68;hpb=7cb2846e682af69c598f6b109dff15a8ea147a1f;p=unres.git

diff --git a/source/cluster/wham/src-HCD-5D/readpdb.F b/source/cluster/wham/src-HCD-5D/readpdb.F
index a7bb52b..58c63e4 100644
--- a/source/cluster/wham/src-HCD-5D/readpdb.F
+++ b/source/cluster/wham/src-HCD-5D/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)