X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Freadpdb.F;h=08c1c2323b56160916ffdf33c029a711034d8967;hb=7675ab8ec26554f2fd3f2e7e427b177254872a45;hp=1d8c3fb12c53553079841818647d43b617a83026;hpb=5715f3ab561c4e22a93fde95d27ad660f46a97b3;p=unres.git

diff --git a/source/unres/src_MD/readpdb.F b/source/unres/src_MD/readpdb.F
index 1d8c3fb..08c1c23 100644
--- a/source/unres/src_MD/readpdb.F
+++ b/source/unres/src_MD/readpdb.F
@@ -16,6 +16,8 @@ C geometry.
       character*3 seq,atom,res
       character*80 card
       dimension sccor(3,20)
+      double precision e1(3),e2(3),e3(3)
+      logical fail
       integer rescode
       ibeg=1
       lsecondary=.false.
@@ -104,9 +106,16 @@ 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)
@@ -128,9 +137,16 @@ 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)
@@ -260,6 +276,9 @@ c      endif
           enddo
           iti=itype(i)
           di=dist(i,nres+i)
+C 10/03/12 Adam: Correction for zero SC-SC bond length
+          if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+     &     di=dsc(itype(i))
           vbld(i+nres)=di
           if (itype(i).ne.10) then
             vbld_inv(i+nres)=1.0d0/di
@@ -411,4 +430,3 @@ c       print *,vbld(i+1),vbld(i+1+nres)
       enddo
       return
       end
-