X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2Fmolread_zs.F;h=2b9fe8c53742a885140b36b5c30e4f5709c61252;hb=d6044e422fadc338f33bb4111e4f18f00f7c7a37;hp=48ce1893d4a8d1188e08fbb0fcc7a8ea380cc41f;hpb=d4479dd2119d03a168ef9526875205081c53e5a9;p=unres.git

diff --git a/source/wham/src-M/molread_zs.F b/source/wham/src-M/molread_zs.F
index 48ce189..2b9fe8c 100644
--- a/source/wham/src-M/molread_zs.F
+++ b/source/wham/src-M/molread_zs.F
@@ -67,19 +67,25 @@ C Convert sequence to numeric code
           itel(i)=2
         endif
       enddo
+       write (iout,*) "ITEL"
+       do i=1,nres-1
+         write (iout,*) i,itype(i),itel(i)
+       enddo
       call read_bridge
 
       if (with_dihed_constr) then
 
       read (inp,*) ndih_constr
       if (ndih_constr.gt.0) then
-        read (inp,*) ftors
-        write (iout,*) 'FTORS',ftors
-        read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
+C        read (inp,*) ftors
+C        write (iout,*) 'FTORS',ftors
+        read (inp,*) (idih_constr(i),phi0(i),drange(i),ftors(i),
+     &   i=1,ndih_constr)
         write (iout,*)
      &   'There are',ndih_constr,' constraints on phi angles.'
         do i=1,ndih_constr
-          write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
+          write (iout,'(i5,3f8.3)') idih_constr(i),phi0(i),drange(i),
+     &    ftors(i)
         enddo
         do i=1,ndih_constr
           phi0(i)=deg2rad*phi0(i)
@@ -88,7 +94,43 @@ C Convert sequence to numeric code
       endif
 
       endif
-
+      if (with_theta_constr) then
+C with_theta_constr is keyword allowing for occurance of theta constrains
+      read (inp,*) ntheta_constr
+C ntheta_constr is the number of theta constrains
+      if (ntheta_constr.gt.0) then
+C        read (inp,*) ftors
+        read (inp,*) (itheta_constr(i),theta_constr0(i),
+     &  theta_drange(i),for_thet_constr(i),
+     &  i=1,ntheta_constr)
+C the above code reads from 1 to ntheta_constr 
+C itheta_constr(i) residue i for which is theta_constr
+C theta_constr0 the global minimum value
+C theta_drange is range for which there is no energy penalty
+C for_thet_constr is the force constant for quartic energy penalty
+C E=k*x**4 
+C        if(me.eq.king.or..not.out1file)then
+         write (iout,*)
+     &   'There are',ntheta_constr,' constraints on phi angles.'
+         do i=1,ntheta_constr
+          write (iout,'(i5,3f8.3)') itheta_constr(i),theta_constr0(i),
+     &    theta_drange(i),
+     &    for_thet_constr(i)
+         enddo
+C        endif
+        do i=1,ntheta_constr
+          theta_constr0(i)=deg2rad*theta_constr0(i)
+          theta_drange(i)=deg2rad*theta_drange(i)
+        enddo
+C        if(me.eq.king.or..not.out1file)
+C     &   write (iout,*) 'FTORS',ftors
+C        do i=1,ntheta_constr
+C          ii = itheta_constr(i)
+C          thetabound(1,ii) = phi0(i)-drange(i)
+C          thetabound(2,ii) = phi0(i)+drange(i)
+C        enddo
+      endif ! ntheta_constr.gt.0
+      endif! with_theta_constr
       nnt=1
       nct=nres
       if (itype(1).eq.ntyp1) nnt=2
@@ -100,6 +142,9 @@ C Convert sequence to numeric code
         write (iout,'(/a,i3,a)') 'The chain contains',ns,
      &  ' disulfide-bridging cysteines.'
         write (iout,'(20i4)') (iss(i),i=1,ns)
+       if (dyn_ss) then
+          write(iout,*)"Running with dynamic disulfide-bond formation"
+       else
         write (iout,'(/a/)') 'Pre-formed links are:' 
         do i=1,nss
 	  i1=ihpb(i)-nres
@@ -111,7 +156,22 @@ C Convert sequence to numeric code
      &    dhpb(i),ebr,forcon(i)
         enddo
       endif
+      endif
       write (iout,'(a)')
+      if (ns.gt.0.and.dyn_ss) then
+          do i=nss+1,nhpb
+            ihpb(i-nss)=ihpb(i)
+            jhpb(i-nss)=jhpb(i)
+            forcon(i-nss)=forcon(i)
+            dhpb(i-nss)=dhpb(i)
+          enddo
+          nhpb=nhpb-nss
+          nss=0
+          call hpb_partition
+          do i=1,ns
+            dyn_ss_mask(iss(i))=.true.
+          enddo
+      endif
       return
       end
 c-----------------------------------------------------------------------------
@@ -150,10 +210,12 @@ C Check whether the specified bridging residues are cystines.
       do i=1,ns
 	if (itype(iss(i)).ne.1) then
 	  write (iout,'(2a,i3,a)') 
-     &   'Do you REALLY think that the residue ',restyp(iss(i)),i,
+     &   'Do you REALLY think that the residue ',
+     &    restyp(itype(iss(i))),i,
      &   ' can form a disulfide bridge?!!!'
 	  write (*,'(2a,i3,a)') 
-     &   'Do you REALLY think that the residue ',restyp(iss(i)),i,
+     &   'Do you REALLY think that the residue ',
+     &    restyp(itype(iss(i))),i,
      &   ' can form a disulfide bridge?!!!'
          stop
         endif