X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2Freadpdb.f;h=daddd523b58f5da6b4b9726e0bfa60f7f8b0322f;hb=0d0c28ca14abcf99ccb778cdba15a9646736571d;hp=a65709e964639f484c57a459ad9f1ab365e50384;hpb=8f0e89da0301c2e2492a53db5f33e55e0d6f1ad8;p=unres.git

diff --git a/source/wham/src-M/readpdb.f b/source/wham/src-M/readpdb.f
index a65709e..daddd52 100644
--- a/source/wham/src-M/readpdb.f
+++ b/source/wham/src-M/readpdb.f
@@ -26,7 +26,9 @@ C geometry.
           goto 10
         else if (card(:3).eq.'TER') then
 C End current chain
-          ires_old=ires+1 
+c          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
@@ -85,14 +87,51 @@ C system
       nres=ires
       do i=2,nres-1
 c        write (iout,*) i,itype(i)
+
         if (itype(i).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            c(j,i)=(c(j,i-1)+c(j,i+1))/2
-            dc(j,i)=c(j,i)
-          enddo
-        endif
+         if (itype(i+1).eq.ntyp1) then
+C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+C           if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+C            call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+C            if (fail) then
+C              e2(1)=0.0d0
+C              e2(2)=1.0d0
+C              e2(3)=0.0d0
+C            endif !fail
+C            do j=1,3
+C             c(j,i)=c(j,i-1)-1.9d0*e2(j)
+C            enddo
+C           else   !unres_pdb
+           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
+C          if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+C            call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+C            if (fail) then
+C              e2(1)=0.0d0
+C              e2(2)=1.0d0
+C              e2(3)=0.0d0
+C            endif
+C            do j=1,3
+C              c(j,i)=c(j,i+1)-1.9d0*e2(j)
+C            enddo
+C          else !unres_pdb
+           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)
@@ -102,7 +141,7 @@ 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
@@ -120,7 +159,7 @@ 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