X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MIN%2Freadpdb.F;h=08bdf960842fed8bb8b02205c65a366dfb7c910f;hb=5f3214b3b9cd011afb780bcaecdf4b4f95bcbbac;hp=dacd12d2f2b29a8aa6975739283bb4f7e2755e09;hpb=478a9d9a1c99eb3f4bc4ca676ff3162bdd01d633;p=unres.git

diff --git a/source/unres/src_MIN/readpdb.F b/source/unres/src_MIN/readpdb.F
index dacd12d..08bdf96 100644
--- a/source/unres/src_MIN/readpdb.F
+++ b/source/unres/src_MIN/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)=21
         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)
@@ -234,7 +250,20 @@ ctest          stop
         vbld(i+1)=dist(i,i+1)
         vbld_inv(i+1)=1.0d0/vbld(i+1)
         if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
-        if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
+        if (i.gt.2) then
+        if (i.le.nres) phi(i+1)=beta(i-2,i-1,i,i+1)
+        if ((itype(i).ne.10).and.(itype(i-1).ne.10)) then
+         tauangle(3,i+1)=beta(i+nres-1,i-1,i,i+nres)
+        endif
+        if (itype(i-1).ne.10) then
+         tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
+         omicron(1,i)=alpha(i-2,i-1,i-1+nres)
+         omicron(2,i)=alpha(i-1+nres,i-1,i)
+        endif
+        if (itype(i).ne.10) then
+         tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
+        endif
+        endif
       enddo
 c      if (unres_pdb) then
 c        if (itype(1).eq.21) then
@@ -258,6 +287,9 @@ c      endif
           enddo
           iti=itype(i)
           di=dist(i,nres+i)
+C 9/29/12 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
@@ -407,4 +439,3 @@ c       print *,vbld(i+1),vbld(i+1+nres)
       enddo
       return
       end
-