X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Freadpdb.F;h=71daf6f61d28d75727a56878a9ee7a74efe6deec;hb=bf8b3ab324569ca7ae7bb9045ad9358f6826a150;hp=8b6f3313013b7cbd4d6b8de16b44c01aecce859f;hpb=498ca45141dbd80fcebdde113c49e95824055b7c;p=unres.git

diff --git a/source/unres/src_MD-M/readpdb.F b/source/unres/src_MD-M/readpdb.F
index 8b6f331..71daf6f 100644
--- a/source/unres/src_MD-M/readpdb.F
+++ b/source/unres/src_MD-M/readpdb.F
@@ -47,7 +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
@@ -80,7 +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          
@@ -93,7 +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
@@ -119,7 +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
@@ -140,7 +140,7 @@ 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 2/15/2013 by Adam: corrected insertion of the last dummy residue
           call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
@@ -169,7 +169,7 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue
         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
@@ -199,6 +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
@@ -229,7 +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.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)
@@ -245,6 +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)
@@ -364,7 +367,7 @@ 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
@@ -388,6 +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
@@ -447,7 +451,7 @@ 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
@@ -467,7 +471,7 @@ 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 
@@ -546,8 +550,8 @@ 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