DO zmiany czytanie pisanie i cutoff

[unres.git] / source / unres / src_MD-M / readpdb.F

diff --git a/source/unres/src_MD-M/readpdb.F b/source/unres/src_MD-M/readpdb.F
index f2daadd..6b385fe 100644 (file)
--- a/source/unres/src_MD-M/readpdb.F
+++ b/source/unres/src_MD-M/readpdb.F
@@ -46,7 +46,8 @@ crc----------------------------------------
           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
@@ -120,13 +121,49 @@ C system
       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
+           if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+            call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+            if (fail) then
+              e2(1)=0.0d0
+              e2(2)=1.0d0
+              e2(3)=0.0d0
+            endif !fail
+            do j=1,3
+             c(j,i)=c(j,i-1)-1.9d0*e2(j)
+            enddo
+           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     
+          endif   !unres_pdb
+         else     !itype(i+1).eq.ntyp1
+          if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+            call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+            if (fail) then
+              e2(1)=0.0d0
+              e2(2)=1.0d0
+              e2(3)=0.0d0
+            endif
+            do j=1,3
+              c(j,i)=c(j,i+1)-1.9d0*e2(j)
+            enddo
+          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
+          endif !unres_pdb
+         endif !itype(i+1).eq.ntyp1
+        endif  !itype.eq.ntyp1
       enddo
 C Calculate the CM of the last side chain.
       if (unres_pdb) then
@@ -150,11 +187,11 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue
             e2(3)=0.0d0
           endif
           do j=1,3
-            c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+            c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
           enddo
         else
         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
@@ -181,11 +218,11 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue
             e2(3)=0.0d0
           endif
           do j=1,3
-            c(j,1)=c(j,2)-3.8d0*e2(j)
+            c(j,1)=c(j,2)-1.9d0*e2(j)
           enddo
         else
         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