Adam's changes

[unres.git] / source / wham / src-HCD-5D / readpdb.F

diff --git a/source/wham/src-HCD-5D/readpdb.F b/source/wham/src-HCD-5D/readpdb.F
index 855d754..9efc6db 100644 (file)
--- a/source/wham/src-HCD-5D/readpdb.F
+++ b/source/wham/src-HCD-5D/readpdb.F
@@ -20,12 +20,13 @@ C geometry.
       integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old
       double precision dcj
       integer rescode,kkk,lll,icha,cou,kupa,iprzes
-      logical lsecondary
+      logical lsecondary,sccalc
       integer iterter(maxres)
       double precision efree_temp
       iii=0
       ibeg=1
       ishift1=0
+      sccalc=.false.
       do
         read (ipdbin,'(a80)',end=10) card
 !       write (iout,'(a)') card
@@ -66,11 +67,13 @@ C geometry.
             call sccenter(ires,iii,sccor)
           endif
           iii=0
+          sccalc=.true.
         endif
 ! Read free energy
-        if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
+c        if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
 ! Fish out the ATOM cards.
         if (index(card(1:4),'ATOM').gt.0) then  
+          sccalc=.false.
           read (card(12:16),*) atom
 c          write (2,'(a)') card
 !          write (iout,*) "! ",atom," !",ires
@@ -88,12 +91,13 @@ c          write (2,'(a)') card
 !              write (iout,*) "Calculating sidechain center iii",iii
               if (unres_pdb) then
                 do j=1,3
-                  dc(j,ires+nres)=sccor(j,iii)
+                  dc(j,ires_old)=sccor(j,iii)
                 enddo
               else
                 call sccenter(ires_old,iii,sccor)
               endif
               iii=0
+              sccalc=.true.
             endif
 ! Start new residue.
             if (res.eq.'Cl-' .or. res.eq.'Na+') then
@@ -214,7 +218,7 @@ C          endif !unres_pdb
         endif  !itype.eq.ntyp1
       enddo
 C Calculate the CM of the last side chain.
-      call sccenter(ires,iii,sccor)
+      if (.not. sccalc) call sccenter(ires,iii,sccor)
       nsup=nres
       nstart_sup=1
       if (itype(nres).ne.10) then
@@ -321,7 +325,7 @@ c        write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1)
         if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and.
      &    (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then
           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
-          stop
+c          stop
         endif
         vbld(i)=dist(i-1,i)
         vbld_inv(i)=1.0d0/vbld(i)
@@ -800,8 +804,8 @@ C Calculate internal coordinates.
       endif
 C Calculate internal coordinates.
 c      call int_from_cart1(.false.)
-      call int_from_cart(.true.,.true.)
-      call sc_loc_geom(.true.)
+      call int_from_cart(.true.,out_template_coord)
+      call sc_loc_geom(.false.)
       do i=1,nres
         thetaref(i)=theta(i)
         phiref(i)=phi(i)