X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fcluster%2Fwham%2Fsrc-M%2Freadpdb.f;h=d6742c67d0468bab3b2ea022c00505f4b2534a95;hb=d174d7fb88aee4a9122f02ebcda537b868723498;hp=bdc3dc2655607b6df50bd5812ee283a74417e2b8;hpb=f67621e926530255a273102edd0aeb87043fd407;p=unres.git

diff --git a/source/cluster/wham/src-M/readpdb.f b/source/cluster/wham/src-M/readpdb.f
index bdc3dc2..d6742c6 100644
--- a/source/cluster/wham/src-M/readpdb.f
+++ b/source/cluster/wham/src-M/readpdb.f
@@ -22,7 +22,8 @@ C geometry.
           goto 10
         else if (card(:3).eq.'TER') then
 C End current chain
-          ires_old=ires+1 
+          ires_old=ires+2
+          itype(ires_old-1)=ntyp1
           itype(ires_old)=ntyp1
           ibeg=2
 c          write (iout,*) "Chain ended",ires,ishift,ires_old
@@ -82,13 +83,29 @@ C system
       do i=2,nres-1
 c        write (iout,*) i,itype(i)
         if (itype(i).eq.ntyp1) then
+         if (itype(i+1).eq.ntyp1) then
+
 c          write (iout,*) "dummy",i,itype(i)
-          do j=1,3
-            c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
+C          do j=1,3
+C            c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
 c            c(j,i)=(c(j,i-1)+c(j,i+1))/2
-            dc(j,i)=c(j,i)
-          enddo
-        endif
+C            dc(j,i)=c(j,i)
+C          enddo
+           do j=1,3
+             dcj=(c(j,i-2)-c(j,i-3))/2.0
+             c(j,i)=c(j,i-1)+dcj
+             c(j,nres+i)=c(j,i)
+           enddo
+C          endif   !unres_pdb
+         else     !itype(i+1).eq.ntyp1
+           do j=1,3
+            dcj=(c(j,i+3)-c(j,i+2))/2.0
+            c(j,i)=c(j,i+1)-dcj
+            c(j,nres+i)=c(j,i)
+           enddo
+C          endif !unres_pdb
+         endif !itype(i+1).eq.ntyp1
+        endif  !itype.eq.ntyp1
       enddo
 C Calculate the CM of the last side chain.
       call sccenter(ires,iii,sccor)
@@ -98,7 +115,7 @@ C Calculate the CM of the last side chain.
         nres=nres+1
         itype(nres)=ntyp1
         do j=1,3
-          dcj=c(j,nres-2)-c(j,nres-3)
+          dcj=(c(j,nres-2)-c(j,nres-3))/2.0
           c(j,nres)=c(j,nres-1)+dcj
           c(j,2*nres)=c(j,nres)
         enddo
@@ -116,7 +133,7 @@ C Calculate the CM of the last side chain.
         nsup=nsup-1
         nstart_sup=2
         do j=1,3
-          dcj=c(j,4)-c(j,3)
+          dcj=(c(j,4)-c(j,3))/2.0
           c(j,1)=c(j,2)-dcj
           c(j,nres+1)=c(j,1)
         enddo
@@ -224,7 +241,7 @@ C-koniec robienia kopidm
      1          '       ', 6X,'X',11X,'Y',11X,'Z',
      &                          10X,'X',11X,'Y',11X,'Z')
   110 format (a,'(',i3,')',6f12.5)
-
+       enddo
 
 
       ishift_pdb=ishift