X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Freadpdb.F;h=f2daaddb90a8887c232c7997d2ef3877cd4f5f5d;hb=31389e1d082428c71d42d61559ca2620daf6cf8d;hp=edd478e8ec4327cc3924807f4de8abcbf688cf72;hpb=478a9d9a1c99eb3f4bc4ca676ff3162bdd01d633;p=unres.git

diff --git a/source/unres/src_MD-M/readpdb.F b/source/unres/src_MD-M/readpdb.F
index edd478e..f2daadd 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
@@ -45,7 +47,7 @@ crc----------------------------------------
         else if (card(:3).eq.'TER') then
 C End current chain
           ires_old=ires+1 
-          itype(ires_old)=21
+          itype(ires_old)=ntyp1
           ibeg=2
 c          write (iout,*) "Chain ended",ires,ishift,ires_old
           if (unres_pdb) then
@@ -78,7 +80,7 @@ c            write (iout,'(a80)') card
               ishift=ires-1
               if (res.ne.'GLY' .and. res.ne. 'ACE') then
                 ishift=ishift-1
-                itype(1)=21
+                itype(1)=ntyp1
               endif
 c              write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
               ibeg=0          
@@ -91,7 +93,7 @@ c              write (iout,*) "New chain started",ires,ishift
             ires=ires-ishift
 c            write (2,*) "ires",ires," ishift",ishift
             if (res.eq.'ACE') then
-              ity=10
+              itype(ires)=10
             else
               itype(ires)=rescode(ires,res,0)
             endif
@@ -117,7 +119,7 @@ C system
       nres=ires
       do i=2,nres-1
 c        write (iout,*) i,itype(i)
-        if (itype(i).eq.21) then
+        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
@@ -138,11 +140,18 @@ C Calculate the CM of the last side chain.
       nstart_sup=1
       if (itype(nres).ne.10) then
         nres=nres+1
-        itype(nres)=21
+        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)
@@ -160,13 +169,20 @@ C Calculate the CM of the last side chain.
         c(j,nres+1)=c(j,1)
         c(j,2*nres)=c(j,nres)
       enddo
-      if (itype(1).eq.21) then
+      if (itype(1).eq.ntyp1) then
         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)
@@ -213,7 +229,7 @@ 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.21)) 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 +245,8 @@ 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)
@@ -348,7 +366,7 @@ c---------------------------------------------------------------------------
 #endif
       do i=1,nres-1
         iti=itype(i)
-        if (iti.ne.21 .and. itype(i+1).ne.21 .and. 
+        if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and. 
      &      (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
 ctest          stop
@@ -431,7 +449,7 @@ c-------------------------------------------------------------------------------
         enddo
       enddo
       do i=2,nres-1
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           do j=1,3
             dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
           enddo
@@ -451,7 +469,7 @@ c-------------------------------------------------------------------------------
         sinfac2=0.5d0/(1.0d0-costtab(i+1))
         sinfac=dsqrt(sinfac2)
         it=itype(i)
-        if (it.ne.10 .and. itype(i).ne.21) then
+        if (it.ne.10 .and. itype(i).ne.ntyp1) then
 c
 C  Compute the axes of tghe local cartesian coordinates system; store in
 c   x_prime, y_prime and z_prime 
@@ -530,8 +548,8 @@ c---------------------------------------------------------------------------
       do i=1,nres-1
        vbld(i+1)=vbl
        vbld_inv(i+1)=1.0d0/vbld(i+1)
-       vbld(i+1+nres)=dsc(itype(i+1))
-       vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
+       vbld(i+1+nres)=dsc(iabs(itype(i+1)))
+       vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
 c       print *,vbld(i+1),vbld(i+1+nres)
       enddo
       return