X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Freadpdb.F;h=71daf6f61d28d75727a56878a9ee7a74efe6deec;hb=75c81b9dbe2f7e18e73a9d61ee02980790335164;hp=f66a5188a4c5b21fd75e36e0a40adfa3a522df84;hpb=e853e7c7e7922e73411b5b215ad733489e8aede5;p=unres.git

diff --git a/source/unres/src_MD-M/readpdb.F b/source/unres/src_MD-M/readpdb.F
index f66a518..71daf6f 100644
--- a/source/unres/src_MD-M/readpdb.F
+++ b/source/unres/src_MD-M/readpdb.F
@@ -16,7 +16,9 @@ C geometry.
       character*3 seq,atom,res
       character*80 card
       dimension sccor(3,20)
+      double precision e1(3),e2(3),e3(3)
       integer rescode
+      logical fail
       ibeg=1
       lsecondary=.false.
       nhfrag=0
@@ -140,9 +142,16 @@ C Calculate the CM of the last side chain.
         nres=nres+1
         itype(nres)=ntyp1
         if (unres_pdb) then
-          c(1,nres)=c(1,nres-1)+3.8d0
-          c(2,nres)=c(2,nres-1)
-          c(3,nres)=c(3,nres-1)
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+          call refsys(nres-3,nres-2,nres-1,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,nres)=c(j,nres-1)-3.8d0*e2(j)
+          enddo
         else
         do j=1,3
           dcj=c(j,nres-2)-c(j,nres-3)
@@ -164,9 +173,16 @@ C Calculate the CM of the last side chain.
         nsup=nsup-1
         nstart_sup=2
         if (unres_pdb) then
-          c(1,1)=c(1,2)-3.8d0
-          c(2,1)=c(2,2)
-          c(3,1)=c(3,2)
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+          call refsys(2,3,4,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,1)=c(j,2)-3.8d0*e2(j)
+          enddo
         else
         do j=1,3
           dcj=c(j,4)-c(j,3)
@@ -183,6 +199,7 @@ C Calculate internal coordinates.
      &    (c(j,nres+ires),j=1,3)
        enddo
       endif
+C      print *,"before int_from_cart"
       call int_from_cart(.true.,.false.)
       call sc_loc_geom(.true.)
       do i=1,nres
@@ -213,7 +230,7 @@ C Splits to single chain if occurs
       lll=lll+1
 cc      write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
       if (i.gt.1) then
-      if ((itype(i-1).eq.ntyp1)) then
+      if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
       chain_length=lll-1
       kkk=kkk+1
 c       write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
@@ -229,6 +246,8 @@ c       write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
           endif
          enddo
       enddo
+      write (iout,*) chain_length
+      if (chain_length.eq.0) chain_length=nres
       do j=1,3
       chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
       chain_rep(j,chain_length+nres,symetr)
@@ -372,6 +391,7 @@ c          vbld(nres)=3.8d0
 c          vbld_inv(nres)=1.0d0/vbld(2)
 c        endif
 c      endif
+      print *,"A TU2"
       if (lside) then
         do i=2,nres-1
           do j=1,3