X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-HCD-5D%2Freadpdb.F;h=6f4ba5f0bfc9f30fa68d0b4c66ab43732d07323e;hb=79fd686e9d9aaa23e4fda802ee16379470e961d3;hp=83c63abcede45c2f7544f0ee1ddf1dcda2712735;hpb=7cb2846e682af69c598f6b109dff15a8ea147a1f;p=unres.git

diff --git a/source/wham/src-HCD-5D/readpdb.F b/source/wham/src-HCD-5D/readpdb.F
index 83c63ab..6f4ba5f 100644
--- a/source/wham/src-HCD-5D/readpdb.F
+++ b/source/wham/src-HCD-5D/readpdb.F
@@ -27,10 +27,9 @@ C geometry.
       ibeg=1
       ishift1=0
       sccalc=.false.
-      ires=0
       do
         read (ipdbin,'(a80)',end=10) card
-c        write (iout,'(a)') card
+!       write (iout,'(a)') card
         if (card(:5).eq.'HELIX') then
           nhfrag=nhfrag+1
           lsecondary=.true.
@@ -59,7 +58,7 @@ c        write (iout,'(a)') card
           iterter(ires_old)=1
           ishift1=ishift1+1
           ibeg=2
-          write (iout,*) "Chain ended",ires,ishift,ires_old
+!          write (iout,*) "Chain ended",ires,ishift,ires_old
           if (unres_pdb) then
             do j=1,3
               dc(j,ires)=sccor(j,iii)
@@ -92,7 +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)
@@ -120,7 +119,7 @@ c              write (iout,*) "BEG ires",ires
 ! Start a new chain
               ishift=-ires_old+ires-1 !!!!!
               ishift1=ishift1-1    !!!!!
-              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+!              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
               ires=ires-ishift+ishift1
               ires_old=ires
               ibeg=0
@@ -326,7 +325,7 @@ 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
-          stop
+c          stop
         endif
         vbld(i)=dist(i-1,i)
         vbld_inv(i)=1.0d0/vbld(i)
@@ -805,8 +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)